List of usage examples for java.lang Exception getStackTrace
public StackTraceElement[] getStackTrace()
From source file:com.flexive.tests.embedded.SearchEngineTest.java
/** * Tests all available value comparators for the given datatype. Note that no semantic * tests are performed, each comparator is executed with a random value. * * @param name the base property name * @param dataType the datatype of the property * @throws com.flexive.shared.exceptions.FxApplicationException * on search engine errors/*w w w. j a v a 2 s .c o m*/ */ @Test(dataProvider = "testProperties") public void genericConditionTest(String name, FxDataType dataType) throws FxApplicationException { final FxPropertyAssignment assignment = getTestPropertyAssignment(name); final Random random = new Random(0); // need to get some folder IDs for the reference property final List<FxPK> folderPks = getFolderPks(); for (PropertyValueComparator comparator : PropertyValueComparator.getAvailable(dataType)) { for (String prefix : new String[] { TEST_TYPE + "/", TEST_TYPE + "/groupTop/", TEST_TYPE + "/groupTop/groupNested/" }) { final String assignmentName = prefix + getTestPropertyName(name); try { // submit a query with the given property/comparator combination final FxValue value; switch (dataType) { case Reference: value = new FxReference( new ReferencedContent(folderPks.get(random.nextInt(folderPks.size())))); break; case DateRange: // a query is always performed against a particular date, but not a date range value = new FxDate(new Date()); break; case DateTimeRange: value = new FxDateTime(new Date()); break; default: value = dataType.getRandomValue(random, assignment); } new SqlQueryBuilder().condition(assignmentName, comparator, value).getResult(); // no exception thrown, consider it a success } catch (Exception e) { fail("Failed to submit for property " + dataType + " with comparator " + comparator + ":\n" + e.getMessage() + ", thrown at:\n" + StringUtils.join(e.getStackTrace(), '\n')); } } } }
From source file:base.BasePlayer.AminoTable.java
void getAminos(Gene gene) { try {/*from w ww . j a va2 s. c o m*/ aminoarray.clear(); VarNode varnode = null; Map.Entry<String, ArrayList<SampleNode>> entry; for (int t = 0; t < gene.varnodes.size(); t++) { varnode = gene.varnodes.get(t); if (gene.intergenic) { for (int v = 0; v < varnode.vars.size(); v++) { entry = varnode.vars.get(v); mutcount = 0; for (int m = 0; m < entry.getValue().size(); m++) { if (entry.getValue().get(m).alleles != null) { break; } if (entry.getValue().get(m).getSample().annotation) { entry.getValue().remove(m); m--; continue; } if (!Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1) && !entry.getValue().get(m).getSample().annotation) { if (!VariantHandler.none.isSelected()) { if (!entry.getValue().get(m).inheritance) { if (!entry.getValue().get(m).getSample() .equals(Main.drawCanvas.selectedSample)) { entry.getValue().remove(m); m--; continue; } } //mutcount++; } if (VariantHandler.onlyselected.isSelected()) { if (!entry.getValue().get(m).getSample() .equals(Main.drawCanvas.selectedSample)) { entry.getValue().remove(m); m--; continue; } } mutcount++; } else { entry.getValue().remove(m); m--; } } if (mutcount == 0) { continue; } base = entry.getKey(); String[] addrow = new String[9]; if (varnode.getTranscripts() == null) { addrow[0] = gene.getName(); } else if (varnode.getTranscripts().size() == 2) { addrow[0] = gene.getName() + " ... " + varnode.getTranscripts().get(1).getGenename(); } else if (varnode.getPosition() < gene.getStart()) { addrow[0] = "... " + varnode.getTranscripts().get(1).getGenename(); } else { addrow[0] = gene.getName() + " ..."; } addrow[1] = "" + mutcount; addrow[2] = gene.getChrom() + ":" + MethodLibrary.formatNumber((varnode.getPosition() + 1)); addrow[3] = "Intergenic"; if (varnode.isRscode() != null) { addrow[4] = varnode.rscode; } else { addrow[4] = "N/A"; } addrow[5] = base; addrow[6] = "Intergenic"; addrow[7] = "Intergenic"; addrow[8] = "Intergenic"; AminoEntry aminoentry = new AminoEntry(addrow, varnode); aminoarray.add(aminoentry); } continue; } if (varnode.getExons() != null) { // for(int exon = 0; exon<varnode.getExons().size(); exon++) { /* if(!VariantHandler.allIsoforms.isSelected() && varnode.getExons().get(exon).getTranscript().getGene().getCanonical() != null && !varnode.getExons().get(exon).getTranscript().isCanonical()) { continue; }*/ /*if(!gene.equals(varnode.getExons().get(exon).getTranscript().getGene())) { continue; } */ if (!varnode.coding && !VariantHandler.utr.isSelected()) { continue; } for (int v = 0; v < varnode.vars.size(); v++) { entry = varnode.vars.get(v); mutcount = 0; for (int m = 0; m < entry.getValue().size(); m++) { if (entry.getValue().get(m).alleles != null) { continue; } if (entry.getValue().get(m).getSample().annotation) { continue; } if (!VariantHandler.none.isSelected()) { if (!entry.getValue().get(m).inheritance) { entry.getValue().remove(m); m--; continue; } } if (!Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) { if (VariantHandler.onlyselected.isSelected()) { if (!entry.getValue().get(m).getSample() .equals(Main.drawCanvas.selectedSample)) { entry.getValue().remove(m); m--; continue; } } mutcount++; } else { entry.getValue().remove(m); m--; } } if (mutcount == 0) { continue; } base = entry.getKey(); String[] addrow = new String[9]; StringBuffer aminos = new StringBuffer(""), transcripts = new StringBuffer(""), exons = new StringBuffer(""), biotypes = new StringBuffer(""); addrow[0] = gene.getName(); addrow[1] = "" + mutcount; addrow[2] = gene.getChrom() + ":" + MethodLibrary.formatNumber((varnode.getPosition() + 1)); String aminochange; for (int exon = 0; exon < varnode.getExons().size(); exon++) { if (!varnode.getExons().get(exon).getTranscript().getGene().equals(gene)) { continue; } aminochange = Main.chromDraw.getAminoChange(varnode, base, varnode.getExons().get(exon)); if (aminochange.contains("UTR") && !VariantHandler.utr.isSelected()) { continue; } if (VariantHandler.nonsense.isSelected()) { if (!MethodLibrary.aminoEffect(aminochange).contains("nonsense")) { continue; } } else if (VariantHandler.synonymous.isSelected()) { if (MethodLibrary.aminoEffect(aminochange).contains("synonymous")) { continue; } } if (aminos.length() == 0) { aminos.append(aminochange); transcripts.append(varnode.getExons().get(exon).getTranscript().getENST()); biotypes.append(varnode.getExons().get(exon).getTranscript().getBiotype()); exons.append(varnode.getExons().get(exon).getNro()); } else { aminos.append(";" + aminochange); transcripts.append(";" + varnode.getExons().get(exon).getTranscript().getENST()); biotypes.append(";" + varnode.getExons().get(exon).getTranscript().getBiotype()); exons.append(";" + varnode.getExons().get(exon).getNro()); } } addrow[3] = aminos.toString(); if (varnode.isRscode() != null) { addrow[4] = varnode.rscode; } else { addrow[4] = "N/A"; } addrow[5] = base; addrow[6] = transcripts.toString(); addrow[7] = biotypes.toString(); addrow[8] = exons.toString(); // varAdd.putNext(null); // varAdd.putPrev(null); AminoEntry aminoentry = new AminoEntry(addrow, varnode); /*if(varnode.getPosition() == 127796784) { System.out.println("Jou"); }*/ aminoarray.add(aminoentry); } // } } if (VariantHandler.intronic.isSelected() && varnode.isInGene() && varnode.getTranscripts() != null && varnode.getExons() == null) { for (int v = 0; v < varnode.vars.size(); v++) { entry = varnode.vars.get(v); base = entry.getKey(); mutcount = 0; for (int m = 0; m < entry.getValue().size(); m++) { if (entry.getValue().get(m).alleles != null) { break; } if (entry.getValue().get(m).getSample().annotation) { entry.getValue().remove(m); m--; continue; } if (!Main.drawCanvas.hideVar(entry.getValue().get(m), entry.getKey().length() > 1)) { if (VariantHandler.onlyselected.isSelected()) { if (!entry.getValue().get(m).getSample() .equals(Main.drawCanvas.selectedSample)) { entry.getValue().remove(m); m--; continue; } } mutcount++; } else { entry.getValue().remove(m); m--; } } if (mutcount == 0) { continue; } StringBuffer transcripts = new StringBuffer(""), biotypes = new StringBuffer(""); String[] addrow = new String[9]; addrow[0] = gene.getName(); addrow[1] = "" + mutcount; addrow[2] = gene.getChrom() + ":" + MethodLibrary.formatNumber((varnode.getPosition() + 1)); addrow[3] = Main.getBase.get(varnode.getRefBase()) + "->" + base + " (intronic)"; if (varnode.isRscode() != null) { addrow[4] = varnode.rscode; } else { addrow[4] = "N/A"; } addrow[5] = base; for (int trans = 0; trans < varnode.getTranscripts().size(); trans++) { if (!varnode.getTranscripts().get(trans).getGene().equals(gene)) { continue; } if (transcripts.length() == 0) { transcripts.append(varnode.getTranscripts().get(trans).getENST()); biotypes.append(varnode.getTranscripts().get(trans).getBiotype()); } else { transcripts.append(";" + varnode.getTranscripts().get(trans).getENST()); biotypes.append(";" + varnode.getTranscripts().get(trans).getBiotype()); } } if (varnode.isRscode() != null) { addrow[4] = varnode.rscode; } else { addrow[4] = "N/A"; } addrow[5] = base; addrow[6] = transcripts.toString(); addrow[7] = biotypes.toString(); addrow[8] = "Intronic"; AminoEntry aminoentry = new AminoEntry(addrow, varnode); aminoarray.add(aminoentry); } } } varnode = null; } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } }
From source file:com.chinamobile.bcbsp.sync.GeneralSSController.java
@Override public void cleanup() { List<String> list = new ArrayList<String>(); List<String> tmpList = new ArrayList<String>(); try {/*from www . ja v a 2 s . co m*/ try { list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-s", false); for (String e : list) { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-s" + "/" + e, bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-s" + "/" + e, false) .getVersion()); } } catch (Exception e) { LOG.info("The exception is " + e.getStackTrace()); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-s", bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-s", false).getVersion()); } jip.reportLOG(jobId.toString() + "delete the -s"); try { list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-d", false); for (String e : list) { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-d" + "/" + e, bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-d" + "/" + e, false) .getVersion()); } } catch (Exception e) { LOG.info("The exception is " + e.getStackTrace()); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-d", bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-d", false).getVersion()); } jip.reportLOG(jobId.toString() + "delete the -d"); try { list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-migrate", false); for (String e : list) { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-migrate" + "/" + e, bspzk.exists( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-migrate" + "/" + e, false).getVersion()); } } catch (Exception e) { LOG.info("The exception is " + e.getStackTrace()); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-migrate", bspzk.exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-migrate", false) .getVersion()); } jip.reportLOG(jobId.toString() + "delete the -migrate"); list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss", false); for (String e : list) { try { tmpList.clear(); tmpList = bspzk.getChildren( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss" + "/" + e, false); for (String ee : tmpList) { bspzk.delete( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss" + "/" + e + "/" + ee, bspzk.exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss" + "/" + e + "/" + ee, false).getAversion()); } } catch (Exception exc) { exc.printStackTrace(); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss" + "/" + e, bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss" + "/" + e, false) .getVersion()); } } bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss", bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-ss", false).getVersion()); jip.reportLOG(jobId.toString() + "delete the -ss"); list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc", false); for (String e : list) { try { tmpList.clear(); tmpList = bspzk.getChildren( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc" + "/" + e, false); for (String ee : tmpList) { bspzk.delete( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc" + "/" + e + "/" + ee, bspzk.exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc" + "/" + e + "/" + ee, false).getAversion()); } } catch (Exception exc) { LOG.info("The exception is " + exc.getStackTrace()); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc" + "/" + e, bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc" + "/" + e, false) .getVersion()); } } bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc", bspzk .exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-sc", false).getVersion()); jip.reportLOG(jobId.toString() + "delete the -sc"); list.clear(); list = bspzk.getChildren(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters", false); for (String e : list) { try { tmpList.clear(); tmpList = bspzk.getChildren( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters" + "/" + e, false); for (String ee : tmpList) { bspzk.delete( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters" + "/" + e + "/" + ee, bspzk.exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters" + "/" + e + "/" + ee, false).getAversion()); } } catch (Exception exc) { LOG.info("The exception is " + exc.getStackTrace()); } finally { bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters" + "/" + e, bspzk.exists( this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters" + "/" + e, false).getVersion()); } } bspzk.delete(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters", bspzk.exists(this.bspZKRoot + "/" + jobId.toString().substring(17) + "-counters", false) .getVersion()); jip.reportLOG(jobId.toString() + "delete the -counters"); } catch (Exception e) { throw new RuntimeException(e); } }
From source file:jp.furplag.util.commons.NumberUtilsTest.java
/** * {@link jp.furplag.util.commons.NumberUtils#valueOf(java.lang.Object, java.lang.Class, boolean)}. */// w ww . ja v a2 s. com @SuppressWarnings("unchecked") @Test public void testValueOfObjectClassOfTBoolean() { assertEquals("null", null, valueOf(null, null, false)); assertEquals("null: fallback", null, valueOf(null, null, true)); try { for (Class<?> type : NUMBERS) { Object o = null; Object expected = null; Class<? extends Number> wrapper = (Class<? extends Number>) ClassUtils.primitiveToWrapper(type); if (type.isPrimitive()) expected = wrapper.getMethod("valueOf", String.class).invoke(null, "0"); assertEquals("null: " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "0"); } else { expected = wrapper.getField("ZERO").get(null); } assertEquals("null: fallback: " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("null: typeEquals: " + type.getSimpleName(), ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = Float.NaN; expected = !type.isPrimitive() ? null : wrapper.getMethod("valueOf", String.class).invoke(null, "0"); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) expected = wrapper.getMethod("valueOf", String.class).invoke(null, "NaN"); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "NaN"); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "0"); } else { expected = wrapper.getField("ZERO").get(null); } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = Double.NaN; expected = !type.isPrimitive() ? null : wrapper.getMethod("valueOf", String.class).invoke(null, "0"); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) expected = wrapper.getMethod("valueOf", String.class).invoke(null, "NaN"); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "NaN"); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "0"); } else { expected = wrapper.getField("ZERO").get(null); } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "1"); } else { expected = wrapper.getField("ONE").get(null); } for (Class<?> valueType : OBJECTS) { if (ClassUtils.isPrimitiveWrapper(valueType)) { o = valueType.getMethod("valueOf", String.class).invoke(null, "1"); } else { o = valueType.getField("ONE").get(null); } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); } if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "-123"); } else { Constructor<?> c = type.getDeclaredConstructor(String.class); expected = c.newInstance("-123"); } for (Class<?> valueType : OBJECTS) { if (ClassUtils.isPrimitiveWrapper(valueType)) { o = valueType.getMethod("valueOf", String.class).invoke(null, "-123"); } else { Constructor<?> c = valueType.getDeclaredConstructor(String.class); o = c.newInstance("-123"); } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); } if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "123.456"); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "123"); } else { Constructor<?> c = type.getDeclaredConstructor(String.class); expected = c.newInstance(BigInteger.class.equals(type) ? "123" : "123.456"); } for (Class<?> valueType : OBJECTS) { if (ObjectUtils.isAny(valueType, Double.class, Float.class)) { o = valueType.getMethod("valueOf", String.class).invoke(null, "123.456"); } else if (BigDecimal.class.equals(valueType)) { Constructor<?> c = valueType.getDeclaredConstructor(String.class); o = c.newInstance("123.456"); } else { continue; } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); } if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "-123.456"); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "-123"); } else { Constructor<?> c = type.getDeclaredConstructor(String.class); expected = c.newInstance(BigInteger.class.equals(type) ? "-123" : "-123.456"); } for (Class<?> valueType : OBJECTS) { if (ObjectUtils.isAny(valueType, Double.class, Float.class)) { o = valueType.getMethod("valueOf", String.class).invoke(null, "-123.456"); } else if (BigDecimal.class.equals(valueType)) { Constructor<?> c = valueType.getDeclaredConstructor(String.class); o = c.newInstance("-123.456"); } else { continue; } assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals(o + "(" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals(o + "(" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); } o = INFINITY_DOUBLE.pow(2); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("POSITIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MAX_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.pow(2).toBigInteger() : INFINITY_DOUBLE.pow(2); } assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("Huge: (" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = INFINITY_DOUBLE.pow(2).negate(); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("NEGATIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MIN_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.pow(2).toBigInteger().negate() : INFINITY_DOUBLE.pow(2).negate(); } assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("Huge: (" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = INFINITY_DOUBLE.pow(2).toBigInteger(); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("POSITIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MAX_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.pow(2).toBigInteger() : INFINITY_DOUBLE.pow(2); } assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("Huge: (" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = INFINITY_DOUBLE.pow(2).toBigInteger().negate(); if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("NEGATIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MIN_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.pow(2).toBigInteger().negate() : INFINITY_DOUBLE.pow(2).negate(); } assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("Huge: (" + o.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("Huge: (" + o.getClass() + "): typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = ""; expected = !type.isPrimitive() ? null : wrapper.getMethod("valueOf", String.class).invoke(null, "0"); assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "0"); } else { expected = wrapper.getField("ZERO").get(null); } assertEquals("\"" + o + "\": fallback: " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("\"" + o + "\": typeEquals: " + type.getSimpleName(), ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = "1"; if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "1"); } else { expected = wrapper.getField("ONE").get(null); } assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("\"" + o + "\": typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = "-123456E-3"; if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "-123.456"); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "-123"); } else { Constructor<?> c = type.getDeclaredConstructor(String.class); expected = c.newInstance(BigInteger.class.equals(type) ? "-123" : "-123.456"); } assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("\"" + o + "\": typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = "Infinity"; if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("POSITIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MAX_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.toBigInteger() : INFINITY_DOUBLE; } assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("\"" + o + "\": typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); o = "-Infinity"; if (ObjectUtils.isAny(wrapper, Double.class, Float.class)) { expected = wrapper.getField("NEGATIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MIN_VALUE").get(null); } else { expected = BigInteger.class.equals(type) ? INFINITY_DOUBLE.toBigInteger().negate() : INFINITY_DOUBLE.negate(); } assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, false)); assertEquals("\"" + o + "\": " + type.getSimpleName(), expected, valueOf(o, (Class<? extends Number>) type, true)); assertEquals("\"" + o + "\": typeEquals: " + type, ClassUtils.primitiveToWrapper(expected.getClass()), valueOf(o, (Class<? extends Number>) type, true).getClass()); } } catch (Exception e) { e.printStackTrace(); fail(e.getMessage() + "\n" + Arrays.toString(e.getStackTrace())); } }
From source file:jp.furplag.util.commons.NumberUtilsTest.java
/** * {@link jp.furplag.util.commons.NumberUtils.NumberObject} *//*from ww w. jav a 2 s . c o m*/ @SuppressWarnings("unchecked") @Test public void NumberObjectTest() { try { Class<?> numberObject = ClassLoader.getSystemClassLoader() .loadClass(NumberUtils.class.getName() + "$NumberObject"); Constructor<?> c = numberObject.getDeclaredConstructor(Class.class); c.setAccessible(true); Method ofType = numberObject.getMethod("of", Class.class); ofType.setAccessible(true); Method ofN = numberObject.getMethod("of", Number.class); ofN.setAccessible(true); Method parsable = numberObject.getDeclaredMethod("parsable", Number.class); parsable.setAccessible(true); Method contains = numberObject.getDeclaredMethod("contains", Number.class); contains.setAccessible(true); Method valueOf = numberObject.getDeclaredMethod("valueOf", Number.class); valueOf.setAccessible(true); for (Class<?> type : NUMBERS) { Object o = c.newInstance(type); Class<? extends Number> wrapper = (Class<? extends Number>) ClassUtils.primitiveToWrapper(type); Object numob = ofType.invoke(null, type); assertEquals("ofType: " + type.getSimpleName(), o, numob); Number n = null; if (!type.isPrimitive()) { if (ClassUtils.isPrimitiveWrapper(type)) { n = (Number) ClassUtils.primitiveToWrapper(type).getMethod("valueOf", String.class) .invoke(null, "1"); } else { n = (Number) type.getField("ONE").get(null); } if (type.equals(byte.class)) assertEquals("ofN: 1: " + type.getSimpleName(), o, ofN.invoke(null, n)); } assertEquals("parsable: -1: " + type.getSimpleName(), true, parsable.invoke(numob, -1)); assertEquals("parsable: 0: " + type.getSimpleName(), true, parsable.invoke(numob, 0)); assertEquals("parsable: 1: " + type.getSimpleName(), true, parsable.invoke(numob, 1)); assertEquals("parsable: null: " + type.getSimpleName(), !type.isPrimitive(), parsable.invoke(numob, (Number) null)); Object expected = ObjectUtils.isAny(wrapper, Float.class, Double.class, BigDecimal.class, BigInteger.class); assertEquals("parsable: Infinity: Double: " + type.getSimpleName(), expected, parsable.invoke(numob, Double.POSITIVE_INFINITY)); assertEquals("parsable: Infinity: Double: BigDecimal: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_DOUBLE)); assertEquals("parsable: Infinity: Double: BigInteger: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_DOUBLE.toBigInteger())); assertEquals("parsable: Infinity: Float: " + type.getSimpleName(), expected, parsable.invoke(numob, Float.POSITIVE_INFINITY)); assertEquals("parsable: Infinity: Float: BigDecimal: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_FLOAT)); assertEquals("parsable: Infinity: Float: BigInteger: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_FLOAT.toBigInteger())); assertEquals("parsable: -Infinity: Double: " + type.getSimpleName(), expected, parsable.invoke(numob, Double.NEGATIVE_INFINITY)); assertEquals("parsable: -Infinity: Double: BigDecimal: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_DOUBLE.negate())); assertEquals("parsable: -Infinity: Double: BigInteger: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_DOUBLE.negate().toBigInteger())); assertEquals("parsable: -Infinity: Float: " + type.getSimpleName(), expected, parsable.invoke(numob, Float.NEGATIVE_INFINITY)); assertEquals("parsable: -Infinity: Float: BigDecimal: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_FLOAT.negate())); assertEquals("parsable: -Infinity: Float: BigInteger: " + type.getSimpleName(), expected, parsable.invoke(numob, INFINITY_FLOAT.negate().toBigInteger())); expected = ObjectUtils.isAny(wrapper, Float.class, Double.class); assertEquals("parsable: NaN: Float: " + type.getSimpleName(), expected, parsable.invoke(numob, Float.NaN)); assertEquals("parsable: NaN: Double: " + type.getSimpleName(), expected, parsable.invoke(numob, Double.NaN)); if (Byte.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MIN_VALUE").getByte(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getByte(null))); assertEquals("parsable: overflow: min: " + type.getSimpleName(), false, parsable.invoke(numob, Short.MIN_VALUE)); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, Short.MAX_VALUE)); assertEquals("parsable: fraction: " + type.getSimpleName(), false, parsable.invoke(numob, 123.456f)); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MIN_VALUE").getByte(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getByte(null))); assertEquals("contains: overflow: min: " + type.getSimpleName(), false, contains.invoke(numob, Short.MIN_VALUE)); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, Short.MAX_VALUE)); assertEquals("contains: fraction: " + type.getSimpleName(), true, contains.invoke(numob, 123.456f)); assertEquals("contains: overflow: fraction: " + type.getSimpleName(), false, contains.invoke(numob, 1234.56f)); } if (Short.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MIN_VALUE").getShort(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getShort(null))); assertEquals("parsable: overflow: min: " + type.getSimpleName(), false, parsable.invoke(numob, Integer.MIN_VALUE)); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, Integer.MAX_VALUE)); assertEquals("parsable: fraction: " + type.getSimpleName(), false, parsable.invoke(numob, 123.456f)); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MIN_VALUE").getShort(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getShort(null))); assertEquals("contains: overflow: min: " + type.getSimpleName(), false, contains.invoke(numob, Integer.MIN_VALUE)); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, Integer.MAX_VALUE)); assertEquals("contains: fraction: " + type.getSimpleName(), true, contains.invoke(numob, 12345.6f)); assertEquals("contains: overflow: fraction: " + type.getSimpleName(), false, contains.invoke(numob, 123456.789f)); } if (Integer.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MIN_VALUE").getInt(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getInt(null))); assertEquals("parsable: overflow: min: " + type.getSimpleName(), false, parsable.invoke(numob, Long.MIN_VALUE)); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, Long.MAX_VALUE)); assertEquals("parsable: fraction: " + type.getSimpleName(), false, parsable.invoke(numob, 123456.789f)); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MIN_VALUE").getInt(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getInt(null))); assertEquals("contains: overflow: min: " + type.getSimpleName(), false, contains.invoke(numob, Long.MIN_VALUE)); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, Long.MAX_VALUE)); assertEquals("contains: fraction: " + type.getSimpleName(), true, contains.invoke(numob, 123456.789f)); assertEquals("contains: overflow: fraction: " + type.getSimpleName(), false, contains.invoke(numob, 12345678912345678912.3456d)); } if (Long.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MIN_VALUE").getLong(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getLong(null))); assertEquals("parsable: overflow: min: " + type.getSimpleName(), false, parsable.invoke(numob, BigInteger.valueOf(Long.MIN_VALUE).pow(2))); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, BigInteger.valueOf(Long.MAX_VALUE).pow(2))); assertEquals("parsable: fraction: " + type.getSimpleName(), false, parsable.invoke(numob, 123.456f)); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MIN_VALUE").getLong(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getLong(null))); assertEquals("contains: overflow: min: " + type.getSimpleName(), false, contains.invoke(numob, BigInteger.valueOf(Long.MIN_VALUE).pow(2))); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, BigInteger.valueOf(Long.MAX_VALUE).pow(2))); assertEquals("contains: fraction: " + type.getSimpleName(), true, contains.invoke(numob, 123456.789f)); assertEquals("contains: overflow: fraction: " + type.getSimpleName(), false, contains.invoke(numob, 12345678912345678912.3456f)); } if (Float.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, -wrapper.getField("MAX_VALUE").getFloat(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getFloat(null))); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, -Double.MAX_VALUE)); assertEquals("parsable: overflow: max: " + type.getSimpleName(), false, parsable.invoke(numob, Double.MAX_VALUE)); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, -wrapper.getField("MAX_VALUE").getFloat(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getFloat(null))); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, -Double.MAX_VALUE)); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, Double.MAX_VALUE)); } if (Double.class.equals(wrapper)) { assertEquals("parsable: contains: min: " + type.getSimpleName(), true, parsable.invoke(numob, -wrapper.getField("MAX_VALUE").getDouble(null))); assertEquals("parsable: contains: max: " + type.getSimpleName(), true, parsable.invoke(numob, wrapper.getField("MAX_VALUE").getDouble(null))); assertEquals("parsable: overflow: min: " + type.getSimpleName(), true, parsable.invoke(numob, INFINITY_DOUBLE.multiply(BigDecimal.TEN).negate())); assertEquals("parsable: overflow: max: " + type.getSimpleName(), true, parsable.invoke(numob, INFINITY_DOUBLE.multiply(BigDecimal.TEN))); assertEquals("contains: min: " + type.getSimpleName(), true, contains.invoke(numob, -wrapper.getField("MAX_VALUE").getDouble(null))); assertEquals("contains: max: " + type.getSimpleName(), true, contains.invoke(numob, wrapper.getField("MAX_VALUE").getDouble(null))); assertEquals("contains: overflow: min: " + type.getSimpleName(), false, contains.invoke(numob, INFINITY_DOUBLE.multiply(BigDecimal.TEN).negate())); assertEquals("contains: overflow: max: " + type.getSimpleName(), false, contains.invoke(numob, INFINITY_DOUBLE.multiply(BigDecimal.TEN))); } if (!ClassUtils.isPrimitiveWrapper(wrapper)) { assertEquals("parsable: fraction: " + type.getSimpleName(), BigDecimal.class.equals(type), parsable.invoke(numob, 123.456f)); assertEquals("contains: fraction: " + type.getSimpleName(), true, contains.invoke(numob, 123.456f)); } if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, "123"); } else { expected = new BigDecimal("123"); if (BigInteger.class.equals(wrapper)) expected = ((BigDecimal) expected).toBigInteger(); } for (Class<?> valueType : OBJECTS) { if (ClassUtils.isPrimitiveWrapper(valueType)) { n = (Number) valueType.getMethod("valueOf", String.class).invoke(null, "123"); } else { n = new BigDecimal("123"); if (BigInteger.class.equals(valueType)) n = ((BigDecimal) n).toBigInteger(); } assertEquals( "valueOf: " + n + " (" + n.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf.invoke(numob, n)); assertEquals( "valueOf: " + n + " (" + n.getClass().getSimpleName() + "): class: " + type.getSimpleName(), expected.getClass(), valueOf.invoke(numob, n).getClass()); } n = 123.456f; if (ObjectUtils.isAny(wrapper, Float.class, Double.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, n.toString()); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, Integer.toString(((Float) n).intValue())); } else { expected = new BigDecimal(n.toString()); if (BigInteger.class.equals(wrapper)) expected = ((BigDecimal) expected).toBigInteger(); } assertEquals("valueOf: " + n + " (" + n.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf.invoke(numob, n)); assertEquals( "valueOf: " + n + " (" + n.getClass().getSimpleName() + "): class: " + type.getSimpleName(), expected.getClass(), valueOf.invoke(numob, n).getClass()); n = 1.23456789E-6d; if (ObjectUtils.isAny(wrapper, Float.class, Double.class)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, n.toString()); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getMethod("valueOf", String.class).invoke(null, Integer.toString(((Double) n).intValue())); } else { expected = new BigDecimal(n.toString()); if (BigInteger.class.equals(wrapper)) expected = ((BigDecimal) expected).toBigInteger(); } assertEquals("valueOf: " + n + " (" + n.getClass().getSimpleName() + "): " + type.getSimpleName(), expected, valueOf.invoke(numob, n)); assertEquals( "valueOf: " + n + " (" + n.getClass().getSimpleName() + "): class: " + type.getSimpleName(), expected.getClass(), valueOf.invoke(numob, n).getClass()); n = INFINITY_DOUBLE.pow(2); if (ObjectUtils.isAny(wrapper, Float.class, Double.class)) { expected = wrapper.getField("POSITIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MAX_VALUE").get(null); } else { expected = new BigDecimal(n.toString()); if (BigInteger.class.equals(wrapper)) expected = ((BigDecimal) expected).toBigInteger(); } assertEquals("valueOf: Huge: " + type.getSimpleName(), expected, valueOf.invoke(numob, n)); assertEquals("valueOf: Huge: class: " + type.getSimpleName(), expected.getClass(), valueOf.invoke(numob, n).getClass()); n = INFINITY_DOUBLE.pow(2).negate(); if (ObjectUtils.isAny(wrapper, Float.class, Double.class)) { expected = wrapper.getField("NEGATIVE_INFINITY").get(null); } else if (ClassUtils.isPrimitiveWrapper(wrapper)) { expected = wrapper.getField("MIN_VALUE").get(null); } else { expected = new BigDecimal(n.toString()); if (BigInteger.class.equals(wrapper)) expected = ((BigDecimal) expected).toBigInteger(); } assertEquals("valueOf: Huge: negative: " + type.getSimpleName(), expected, valueOf.invoke(numob, n)); assertEquals("valueOf: Huge: negative: class: " + type.getSimpleName(), expected.getClass(), valueOf.invoke(numob, n).getClass()); } } catch (Exception e) { e.printStackTrace(); fail(e.getMessage() + "\n" + Arrays.toString(e.getStackTrace())); } }
From source file:com.almalence.plugins.capture.video.VideoCapturePlugin.java
private void createModeSwitcher() { LayoutInflater inflator = ApplicationScreen.instance.getLayoutInflater(); modeSwitcher = (com.almalence.ui.Switch.Switch) inflator .inflate(R.layout.plugin_capture_standard_modeswitcher, null, false); SharedPreferences prefs = PreferenceManager.getDefaultSharedPreferences(ApplicationScreen.getMainContext()); ModePreference = prefs.getString("modeVideoDROPref", "1"); modeSwitcher.setTextOn(ApplicationScreen.instance.getString(R.string.Pref_Video_DRO_ON)); modeSwitcher.setTextOff(ApplicationScreen.instance.getString(R.string.Pref_Video_DRO_OFF)); modeSwitcher.setChecked(ModePreference.compareTo("0") == 0 ? true : false); modeSwitcher.setOnCheckedChangeListener(new CompoundButton.OnCheckedChangeListener() { @Override/*from ww w . j av a2 s .com*/ public void onCheckedChanged(CompoundButton buttonView, boolean isChecked) { SharedPreferences prefs = PreferenceManager .getDefaultSharedPreferences(ApplicationScreen.getMainContext()); if (isChecked) { ModePreference = "0"; if (CameraController.isNexus6) { Toast.makeText(ApplicationScreen.getMainContext(), "Not suported currently on your device. Will be available later.", Toast.LENGTH_LONG).show(); ModePreference = "1"; modeSwitcher.setChecked(false); return; } } else { ModePreference = "1"; } SharedPreferences.Editor editor = prefs.edit(); editor.putString("modeVideoDROPref", ModePreference); editor.commit(); if (modeDRO()) { int quality = Integer.parseInt(prefs.getString( CameraController.getCameraIndex() == 0 ? ApplicationScreen.sImageSizeVideoBackPref : ApplicationScreen.sImageSizeVideoFrontPref, DEFAULT_VIDEO_QUALITY)); if (quality > CamcorderProfile.QUALITY_720P || maxQuality()) { quality = CamcorderProfile.QUALITY_720P; quickControlIconID = R.drawable.gui_almalence_video_720; editor.putString( CameraController.getCameraIndex() == 0 ? ApplicationScreen.sImageSizeVideoBackPref : ApplicationScreen.sImageSizeVideoFrontPref, String.valueOf(quality)); editor.commit(); VideoCapturePlugin.this.refreshQuickControl(); } } try { CameraController.stopCameraPreview(); setCameraPreviewSize(); if (VideoCapturePlugin.this.modeDRO()) { takePictureButton.setVisibility(View.GONE); timeLapseButton.setVisibility(View.GONE); ApplicationScreen.instance.showOpenGLLayer(2); ApplicationScreen.instance.glSetRenderingMode(GLSurfaceView.RENDERMODE_WHEN_DIRTY); } else { if (!CameraController.isRemoteCamera()) { if (displayTakePicture) takePictureButton.setVisibility(View.VISIBLE); timeLapseButton.setVisibility(View.VISIBLE); } droEngine.onPause(); ApplicationScreen.instance.hideOpenGLLayer(); if (!CameraController.isUseCamera2()) { CameraController.setupCamera(ApplicationScreen.getPreviewSurfaceHolder(), true); } CameraController.startCameraPreview(); } } catch (final Exception e) { Log.e(TAG, Util.toString(e.getStackTrace(), '\n')); e.printStackTrace(); } } }); }
From source file:net.naijatek.myalumni.modules.members.presentation.action.MaintainMemberAction.java
public ActionForward addMember(ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { ActionMessages errors = new ActionMessages(); SystemConfigVO sysConfigVO = sysConfigSerivce.getSystemConfig(); try {/*from ww w .j a va 2 s . c om*/ MemberForm memberForm = (MemberForm) form; MemberVO memberVO = new MemberVO(); BeanUtils.copyProperties(memberVO, memberForm); memberVO.setLastModifiedBy(memberVO.getMemberUserName()); // Member memService.createMember(memberVO, request); //////// final String memberId = memberVO.getMemberId(); // Messengers List<MessengerVO> messengers = new ArrayList<MessengerVO>(); MessengerVO mesgerVO = null; for (String str : memberVO.getLstSelectedIMs()) { mesgerVO = new MessengerVO(); mesgerVO.setLastModifiedBy(memberVO.getMemberUserName()); mesgerVO.setMemberId(memberId); mesgerVO.setLookupCodeId(str); messengers.add(mesgerVO); } messengerService.saveAll(messengers, memberId); // Message Folders mfService.createMemberMessageFolders(memberId, SystemConfigConstants.MESSAGE_FOLDERS, memberVO.getMemberUserName()); StringBuffer message = new StringBuffer(); message.append("Thank you " + StringUtil.capitalize(memberVO.getFirstName()) + " " + StringUtil.capitalize(memberVO.getLastName()) + " for registering and Welcome to " + sysConfigVO.getOrganizationName() + "'s owns space in cyberspace."); message.append( "Your account should be active within the next 24 hours. So please try logging into the system as soon as you get your activation confirmation email."); setSessionObject(request, BaseConstants.MESSAGE, message.toString()); // send email to registrant try { SendMailUtil.sendWelcomeNotice(memberVO.getEmail(), memberVO.getMemberUserName(), sysConfigVO); } catch (Exception ex) { logger.error(ex.getMessage()); errors.add(BaseConstants.FATAL_KEY, new ActionMessage("error.mailserver")); saveMessages(request, errors); return mapping.findForward(BaseConstants.FWD_SUCCESS); } // send email to administrator about new registrant try { SendMailUtil.notifyAdminAboutNewMember(memberVO, sysConfigVO); } catch (Exception ex) { logger.error(ex.getMessage()); errors.add(BaseConstants.FATAL_KEY, new ActionMessage("error.mailserver")); saveMessages(request, errors); return mapping.findForward(BaseConstants.FWD_SUCCESS); } } catch (DuplicateMemberException e) { errors.add(BaseConstants.WARN_KEY, new ActionMessage("error.duplicate.member")); saveMessages(request, errors); logger.info("DUPLICATE USER NAME - " + e.getMessage()); return mapping.getInputForward(); } catch (DuplicateEmailException e) { errors.add(BaseConstants.WARN_KEY, new ActionMessage("error.duplicate.email")); saveMessages(request, errors); logger.info("DUPLICATE EMAIL - " + e.getMessage()); return mapping.getInputForward(); } catch (CreateException e) { errors.add(BaseConstants.WARN_KEY, new ActionMessage("errors.technical.difficulty")); saveMessages(request, errors); logger.fatal("SYSTEM ERROR - " + e.getMessage()); return mapping.getInputForward(); } catch (Exception ex) { errors.add(BaseConstants.FATAL_KEY, new ActionMessage("errors.technical.difficulty")); saveMessages(request, errors); logger.fatal("SYSTEM ERROR - " + ex.getStackTrace()); return mapping.getInputForward(); } return mapping.findForward(BaseConstants.FWD_SUCCESS); }
From source file:base.BasePlayer.BedTable.java
void drawScreen(Graphics g) { try {/*from w ww . j a v a 2 s. c om*/ buf.setColor(Color.black); buf.fillRect(0, 0, this.getWidth(), this.getHeight()); if (width != this.getWidth()) { width = this.getWidth(); createPolygon(); resizeTable(); } genemutcount = 0; if (!bedtrack.intersect) { buf.setColor(Color.white); buf.drawString("Press play on bed track to annotate variants", 5, 40); } else if (getTableSize() > 0) { hoverVar = null; hoverSample = -1; headerHover = -1; geneHeaderHover = -1; if (!mouseDrag) { resizeColumn = -1; } if (aminoarray == null) { aminoarray = new ArrayList<AminoEntry>(); } firstrow = tablescroll.getVerticalScrollBar().getValue() / rowHeight - samplecount - listAdd - aminoarray.size(); if (firstrow < 0) { firstrow = 0; } for (int i = firstrow; i < bedarray.size(); i++) { dot = false; if ((i + 1 + samplecount + listAdd + aminoarray.size()) * rowHeight < tablescroll .getVerticalScrollBar().getValue()) { continue; } if (i * rowHeight > tablescroll.getVerticalScrollBar().getValue() + tablescroll.getViewport().getHeight()) { break; } if (mouseY >= (rowHeight * (i + genemutcount + 1)) && mouseY < (rowHeight * (i + genemutcount + 2))) { hoverNode = bedarray.get(i); } try { buf.setColor(Color.darkGray); buf.drawLine(4, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } if (bedarray.get(i).getTrack().hasvalues) { buf.drawString( (i + 1) + ". " + MethodLibrary.shortString(bedarray.get(i).name, 10) + "=" + MethodLibrary.round(bedarray.get(i).value, 3), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString((i + 1) + ". " + MethodLibrary.shortString(bedarray.get(i).name, 10), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect( headerlengths[1][0] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, headerlengths[1][1], rowHeight - 1); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } mutcountbuffer = new StringBuffer("" + bedarray.get(i).mutations + " "); buf.drawString(mutcountbuffer.toString(), headerlengths[1][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); // lastpos = Integer.toString(bedarray.get(i).mutations).length() +2; //TODO textWidth = (int)fm.getStringBounds("", buf).getWidth(); // textWidth = (int)fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); // buf.drawString(" ", headerlengths[1][0]+5+textWidth, (rowHeight*(i+1+genemutcount))-tablescroll.getVerticalScrollBar().getValue()+rowHeight); // buf.setColor(Color.gray); // textWidth = (int)fm.getStringBounds(mutcountbuffer.toString() , buf).getWidth(); // buf.drawString(" " +bedarray.get(i).varnodes.size() +" samples", headerlengths[1][0]+5+textWidth, (rowHeight*(i+1+genemutcount))-tablescroll.getVerticalScrollBar().getValue()+rowHeight); buf.setColor(Color.black); buf.fillRect( headerlengths[2][0] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } buf.drawString( bedarray.get(i).getChrom() + ":" + MethodLibrary.formatNumber(bedarray.get(i).getPosition() + 1) + "-" + MethodLibrary.formatNumber( bedarray.get(i).getPosition() + 1 + bedarray.get(i).getLength()), headerlengths[2][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( headerlengths[3][0] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } buf.drawString(MethodLibrary.formatNumber(bedarray.get(i).getLength()), headerlengths[3][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( headerlengths[4][0] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } buf.drawString("" + MethodLibrary .round((bedarray.get(i).mutations / (double) bedarray.get(i).getLength()) * 100, 4), headerlengths[4][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( headerlengths[5][0] + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (bedarray.get(i).equals(hoverNode) || bedarray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } firstvisible = 0; if (bedarray.get(i).varnodes != null) { for (int f = 0; f < bedarray.get(i).varnodes.size(); f++) { if (!Main.drawCanvas.hideNode(bedarray.get(i).varnodes.get(f))) { firstvisible = f; break; } } if (bedarray.get(i).varnodes.get(firstvisible).getExons() != null) { if (bedarray.get(i).varnodes.get(firstvisible).coding) { buf.setColor(Color.red); buf.drawString( bedarray.get(i).varnodes.get(firstvisible).getExons().get(0) .getTranscript().getGenename() + " (Coding)", headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.lightGray); buf.drawString( bedarray.get(i).varnodes.get(firstvisible).getExons().get(0) .getTranscript().getGenename() + " (UTR)", headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } else if (bedarray.get(i).varnodes.get(firstvisible).isInGene()) { buf.setColor(Color.lightGray); buf.drawString( bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(0) .getGenename() + " (Intronic)", headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.gray); if (!bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(0).equals( bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(1))) { buf.drawString( bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(0) .getGenename() + " ... " + bedarray.get(i).varnodes.get(firstvisible).getTranscripts() .get(1).getGenename(), headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { if (bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(0) .getEnd() > bedarray.get(i).varnodes.get(firstvisible).getPosition()) { buf.drawString( " ... " + bedarray.get(i).varnodes.get(firstvisible) .getTranscripts().get(0).getGenename(), headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString( bedarray.get(i).varnodes.get(firstvisible).getTranscripts().get(0) .getGenename() + " ... ", headerlengths[5][0] + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } buf.setColor(Color.darkGray); buf.drawLine(3, rowHeight + 3, 3, (rowHeight * (i + genemutcount + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); for (int r = 0; r < headerlengths.length; r++) { buf.drawLine(headerlengths[r][0], (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, headerlengths[r][0], (rowHeight * (i + genemutcount + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); } if (selectedNode != null && selectedNode.equals(bedarray.get(i))) { hoverSample = -1; genemutcount = aminoarray.size() + 1; listAdd = 1; buf.drawLine(20, (rowHeight * (i + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); drawGeneheader((rowHeight * (i + listAdd + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); for (int s = 0; s < aminoarray.size(); s++) { buf.setColor(Color.darkGray); buf.drawLine(21, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); if (mouseY >= (rowHeight * (i + s + listAdd + 2)) && mouseY < (rowHeight * (i + s + listAdd + 3))) { hoverNode = null; hoverVar = aminoarray.get(s).getNode(); hoverString = aminoarray.get(s).getRow(); buf.setColor(Color.white); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { hoverSample = aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .getSample().getIndex(); break; } } } else { if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("nonsense")) { buf.setColor(Color.red); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("missense")) { buf.setColor(Color.yellow); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("synonymous")) { buf.setColor(Color.green); } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("UTR")) { buf.setColor(Color.lightGray); } else { buf.setColor(Color.gray); } } if (!aminoarray.get(s).getRow()[1].equals("1")) { buf.drawString("Multiple", 24, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { buf.drawString( aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .getSample().getName(), 24, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); break; } } } if (hoverVar != null && hoverString.equals(aminoarray.get(s).getRow())) { //TODO textcolor = Color.white; } else { if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("nonsense")) { textcolor = Color.red; } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("missense")) { textcolor = Color.yellow; } else if (MethodLibrary.aminoEffect(aminoarray.get(s).getRow()[3]) .equals("synonymous")) { textcolor = Color.green; } else if (aminoarray.get(s).getRow()[3].contains("UTR")) { textcolor = Color.lightGray; } else { textcolor = Color.gray; } } for (int h = 1; h < 4; h++) { buf.setColor(Color.black); buf.fillRect((int) geneheader.get(h)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(h)[2], rowHeight - 1); buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[h], (int) geneheader.get(h)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } if (aminoarray.get(s).getRow()[1].equals("1")) { buf.setColor(Color.black); buf.fillRect((int) geneheader.get(4)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { if (aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .isHomozygous()) { buf.drawString( "Hom (" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 2; casefreq = 2 / (double) (Main.varsamples * 2); } } else { buf.drawString( "Het (" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(0).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 1; casefreq = 1 / (double) (Main.varsamples * 2); } } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(5)[1] + 1, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + aminoarray.get(s).getNode().vars .get(v).getValue().get(0).getQuality(), (int) geneheader.get(5)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } if (Control.controlData.controlsOn) { cases = 0; for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { if (aminoarray.get(s).getNode().vars.get(v).getValue().get(0) .isHomozygous()) { cases += Integer.parseInt(aminoarray.get(s).getRow()[1]) * 2; } else { cases += Integer.parseInt(aminoarray.get(s).getRow()[1]); } } } casefreq = cases / (double) (Main.varsamples * 2); } buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[4], (int) geneheader.get(6)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { buf.setColor(textcolor); for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(aminoarray.get(s).getRow()[5])) { vararray = aminoarray.get(s).getNode().vars.get(v).getValue(); controlarray = new SampleNode[Control.controlData.fileArray.size()]; if (vararray.get(vararray.size() - 1).alleles != null) { for (int e = vararray.size() - 1; e > 0; e--) { if (vararray.get(e).alleles == null) { break; } controlarray[vararray.get(e).getControlSample() .getIndex()] = vararray.get(e); } } for (int e = 0; e < controlarray.length; e++) { if (Control.controlData.fileArray.get(e).controlOn) { if (controlarray[e] == null) { buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("0", (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("-", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); } else { buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + MethodLibrary.round(controlarray[e].alleles / (double) controlarray[e].allelenumber, 2), (int) geneheader .get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString("" + MethodLibrary .round(casefreq / (controlarray[e].alleles / (double) controlarray[e].allelenumber), 2) + " (p=" + MethodLibrary.round( VariantHandler.table.fe.getRightTailedP( cases, Main.varsamples * 2 - cases, controlarray[e].alleles, controlarray[e].allelenumber - controlarray[e].alleles), 2) + ")", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll .getVerticalScrollBar().getValue() + rowHeight); } } else { buf.setColor(Color.black); buf.fillRect( (int) geneheader.get(this.geneheaderlength + e * 2)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(Color.darkGray); buf.drawString("Apply controls", (int) geneheader.get(this.geneheaderlength + e * 2)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.black); buf.fillRect( (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 11, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(Color.darkGray); buf.drawString("-", (int) geneheader .get(this.geneheaderlength + e * 2 + 1)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } } else { buf.setColor(Color.darkGray); for (int e = geneheaderlength; e < geneheader.size(); e++) { if (geneheader.get(e)[0] instanceof ControlFile) { buf.drawString("Apply controls", (int) geneheader.get(e)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } buf.setColor(Color.lightGray); } vararray = null; if (Main.bedCanvas.bedOn) { for (int a = 0; a < aminoarray.size(); a++) { StringBuffer[] bedarraytemp = MethodLibrary.makeTrackArray( aminoarray.get(a).getNode(), aminoarray.get(a).getRow()[5]); if (bedarraytemp != null) { int h = 0; for (int b = 0; b < bedarraytemp.length; b++) { if (b == bedtrack.trackIndex) { continue; } buf.setColor(Color.black); if (b == bedarraytemp.length - 1) { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + h)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth() - (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + h)[1], rowHeight - 1); } else { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + h)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + h)[2], rowHeight - 1); } buf.setColor(Color.white); if (bedarraytemp[b] != null) { buf.drawString(bedarraytemp[b].toString(), (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + h)[1] + 14, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } h++; // buf.drawLine((int)geneheader.get(geneheaderlength+Control.controlData.fileArray.size()*2+h)[1], (rowHeight*(i+a+listAdd+2))-tablescroll.getVerticalScrollBar().getValue()+4, (int)geneheader.get(geneheaderlength+Control.controlData.fileArray.size()*2+h)[1], (rowHeight*(i+a+listAdd+2))-tablescroll.getVerticalScrollBar().getValue()+10); } } } } buf.setColor(Color.darkGray); for (int j = 0; j < geneheader.size(); j++) { buf.drawLine((int) geneheader.get(j)[1] + 11, (rowHeight * (i + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); } if (selectedVar != null && selectedString.equals(aminoarray.get(s).getRow()) && Integer.parseInt(selectedString[1]) > 1) { //hoverSample = -1; pointer = 0; //TODO for (int v = 0; v < aminoarray.get(s).getNode().vars.size(); v++) { if (aminoarray.get(s).getNode().vars.get(v).getKey() .equals(selectedString[5])) { for (int l = 0; l < aminoarray.get(s).getNode().vars.get(v).getValue() .size(); l++) { if (aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).alleles != null) { break; } if (mouseY > (rowHeight * (i + s + pointer + 4)) && mouseY < (rowHeight * (i + s + pointer + 5))) { textcolor = Color.white; hoverVar = aminoarray.get(s).getNode(); hoverString = aminoarray.get(s).getRow(); hoverSample = aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).getSample().getIndex(); } else { textcolor = Color.lightGray; } // if(aminoarray.get(s).getNode().getSamples().get(l).getVariation().equals(selectedString[5])) { buf.setColor(textcolor); buf.drawString( aminoarray.get(s).getNode().vars.get(v).getValue().get(l) .getSample().getName(), 30, (rowHeight * (i + s + pointer + 4)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); pointer++; // } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(4)[1] + 10, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); if (aminoarray.get(s).getNode().vars.get(v).getValue().get(l) .isHomozygous()) { buf.drawString( "Hom (" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString( "Het (" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCalls() + "/" + aminoarray.get(s).getNode().vars.get(v) .getValue().get(l).getCoverage() + ")", (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(5)[1] + 10, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); buf.setColor(textcolor); buf.drawString( "" + aminoarray.get(s).getNode().vars.get(v).getValue() .get(l).getQuality(), (int) geneheader.get(5)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.darkGray); for (int j = 4; j < 7; j++) { buf.drawLine((int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue(), (int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight + 2); } } } } listAdd = Integer.parseInt(selectedString[1]) + 1; genemutcount = aminoarray.size() + listAdd; buf.setColor(Color.darkGray); buf.drawLine(21, (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (i + s + listAdd + 3)) - tablescroll.getVerticalScrollBar().getValue() + 3); } } } } catch (Exception e) { ErrorLog.addError(e.getStackTrace()); e.printStackTrace(); } } buf.setColor(Color.darkGray); buf.drawLine(4, (rowHeight * (bedarray.size() + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (bedarray.size() + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3); } drawHeader(); if (headerHover == -1 && geneHeaderHover == -1) { setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } else { if (resizeColumn == -1) { setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR)); } else { setCursor(Cursor.getPredefinedCursor(Cursor.E_RESIZE_CURSOR)); } } g.drawImage(bufImage, 0, tablescroll.getVerticalScrollBar().getValue(), null); } catch (Exception e) { e.printStackTrace(); } }
From source file:ome.services.blitz.fire.SessionManagerI.java
public Glacier2.SessionPrx create(String userId, Glacier2.SessionControlPrx control, Ice.Current current) throws CannotCreateSessionException { if (!loaded.get()) { WrappedCreateSessionException wrapped = new WrappedCreateSessionException(); wrapped.backOff = 1000L;//w ww.j a va 2 s.c o m wrapped.concurrency = true; wrapped.reason = "Server not fully initialized"; wrapped.type = "ApiUsageException"; throw wrapped; } try { // First thing we do is guarantee that the client is giving us // the required information. ServiceFactoryI.clientId(current); // throws ApiUsageException // Before asking the ring, see if we already have the // session locally. boolean local = false; try { Object o = sessionManager.find(userId); local = (o != null); log.info("Found session locally: " + userId); } catch (Exception e) { log.debug("Exception while waiting on " + "SessionManager.find " + e); } // If not, then give the ring a chance to redirect to // other instances which may already have it. if (!local) { Glacier2.SessionPrx sf = ring.getProxyOrNull(userId, control, current); if (sf != null) { return sf; // EARLY EXIT } } // Defaults Roles roles = securitySystem.getSecurityRoles(); String group = getGroup(current); if (group == null) { group = roles.getUserGroupName(); } String event = getEvent(current); if (event == null) { event = "User"; // FIXME This should be in Roles as well. } String agent = getAgent(current); // Create the session for this ServiceFactory Principal p = new Principal(userId, group, event); ome.model.meta.Session s = sessionManager.createWithAgent(p, agent); Principal sp = new Principal(s.getUuid(), group, event); // Event raised to add to Ring // Create the ServiceFactory ServiceFactoryI session = new ServiceFactoryI(local /* ticket:911 */, current, control, context, sessionManager, executor, sp, CPTORS, topicManager, registry); Ice.Identity id = session.sessionId(); if (control != null) { // Not having a control implies that this is an internal // call, not coming through Glacier, so we can trust it. StringSetPrx cat = control.categories(); cat.add(new String[] { id.category }); cat.add(new String[] { id.name }); } Ice.ObjectPrx _prx = current.adapter.add(session, id); // OK Usage _prx = current.adapter.createDirectProxy(id); // Logging & sessionToClientIds addition if (!sessionToClientIds.containsKey(s.getUuid())) { sessionToClientIds.put(s.getUuid(), new HashSet<String>()); log.info(String.format("Created session %s for user %s (agent=%s)", session, userId, agent)); } else { if (log.isInfoEnabled()) { log.info(String.format("Rejoining session %s (agent=%s)", session, agent)); } } sessionToClientIds.get(s.getUuid()).add(session.clientId); return Glacier2.SessionPrxHelper.uncheckedCast(_prx); } catch (Exception t) { // Then we are good to go. if (t instanceof CannotCreateSessionException) { throw (CannotCreateSessionException) t; } // These need special handling as well. else if (t instanceof ome.conditions.ConcurrencyException || t instanceof omero.ConcurrencyException) { // Parse out the back off, then everything is generic. long backOff = (t instanceof omero.ConcurrencyException) ? ((omero.ConcurrencyException) t).backOff : ((ome.conditions.ConcurrencyException) t).backOff; WrappedCreateSessionException wrapped = new WrappedCreateSessionException(); wrapped.backOff = backOff; wrapped.type = t.getClass().getName(); wrapped.concurrency = true; wrapped.reason = "ConcurrencyException: " + t.getMessage() + "\nPlease retry in " + backOff + "ms. Cause: " + t.getMessage(); throw wrapped; } ConvertToBlitzExceptionMessage convert = new ConvertToBlitzExceptionMessage(this, t); try { // TODO Possibly provide context.convert(ConversionMsg) methd. context.publishMessage(convert); } catch (Throwable t2) { log.error("Error while converting exception:", t2); } if (convert.to instanceof CannotCreateSessionException) { throw (CannotCreateSessionException) convert.to; } // We make an exception for some more or less "expected" exception // types. Everything else gets logged as an error which we need // to review. if (!(t instanceof omero.ApiUsageException || t instanceof ome.conditions.ApiUsageException || t instanceof ome.conditions.SecurityViolation)) { log.error("Error while creating ServiceFactoryI", t); } WrappedCreateSessionException wrapped = new WrappedCreateSessionException(); wrapped.backOff = -1; wrapped.concurrency = false; wrapped.reason = t.getMessage(); wrapped.type = t.getClass().getName(); wrapped.setStackTrace(t.getStackTrace()); throw wrapped; } }
From source file:au.org.theark.study.model.dao.StudyDao.java
public void update(Consent consent) throws ArkSystemException, EntityNotFoundException { try {/*w ww .ja v a2s . com*/ Session session = getSession(); session.merge(consent); } catch (HibernateException someHibernateException) { log.error("An Exception occured while trying to update this consent " + someHibernateException.getStackTrace()); } catch (Exception e) { log.error("An Exception occured while trying to update this consent " + e.getStackTrace()); throw new ArkSystemException( "A System Error has occured. We wil have someone contact you regarding this issue"); } }