List of usage examples for java.awt Cursor DEFAULT_CURSOR
int DEFAULT_CURSOR
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From source file:base.BasePlayer.AminoTable.java
void drawScreen(Graphics g) { if (!isEnabled()) { return;/* ww w . j a v a 2 s . co m*/ } buf.setColor(Color.black); buf.fillRect(0, 0, VariantHandler.tableScroll.getViewport().getWidth(), tablescroll.getViewport().getHeight()); if (VariantHandler.writetofile.isSelected()) { buf.setColor(Color.white); if (FileRead.output != null && Main.drawCanvas.loading && Draw.variantcalculator) { buf.drawString("Writing results to " + FileRead.outputName, 10, 20); } else { buf.drawString("Press annotate to write results straight to file", 10, 20); } g.drawImage(bufImage, 0, tablescroll.getVerticalScrollBar().getValue(), null); return; } //Header Draw genemutcount = 0; hoverVar = null; hoverSample = -1; headerHover = -1; geneHeaderHover = -1; if (!mouseDrag) { resizeColumn = -1; } firstrow = tablescroll.getVerticalScrollBar().getValue() / rowHeight - samplecount - listAdd - aminoarray.size(); if (firstrow < 0) { firstrow = 0; } for (int i = 0; i < genearray.size(); i++) { dot = false; if ((i + 1 + samplecount + aminoarray.size() + listAdd) * 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 = genearray.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 (genearray.get(i).equals(hoverNode) || genearray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } textWidth = (int) fm.getStringBounds("" + (i + 1) + ". " + genearray.get(i).getName(), buf) .getWidth(); if (genearray.get(i).intergenic) { if (genearray.get(i).varnodes.get(0).getTranscripts() == null) { buf.drawString((i + 1) + ". " + genearray.get(i).getName(), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (genearray.get(i).varnodes.get(0).getTranscripts().size() == 2) { buf.drawString( (i + 1) + ". " + genearray.get(i).getName() + " ... " + genearray.get(i).varnodes.get(0).getTranscripts().get(1).getGenename(), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (genearray.get(i).varnodes.get(0).getPosition() < genearray.get(i).getStart()) { buf.drawString((i + 1) + ". " + " ... " + genearray.get(i).getName(), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString((i + 1) + ". " + genearray.get(i).getName() + " ... ", 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } else { buf.drawString((i + 1) + ". " + genearray.get(i).getName(), 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) (headerlengths[1][0] + 1), (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) (headerlengths[1][1]), rowHeight - 1); if (genearray.get(i).equals(hoverNode) || genearray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } mutcountbuffer = new StringBuffer("" + genearray.get(i).mutations + " ("); buf.drawString(mutcountbuffer.toString(), (int) (headerlengths[1][0] + 5), (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (genearray.get(i).nonsense > 0) { buf.setColor(Color.red); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString("" + genearray.get(i).nonsense, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(genearray.get(i).nonsense); dot = true; } if (genearray.get(i).missense > 0) { if (dot) { buf.setColor(Color.white); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString(", ", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(", "); } textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.setColor(Color.yellow); buf.drawString("" + genearray.get(i).missense, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(genearray.get(i).missense); dot = true; } if (genearray.get(i).synonymous > 0) { if (dot) { buf.setColor(Color.white); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString(", ", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(", "); } textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.setColor(Color.green); buf.drawString("" + genearray.get(i).synonymous, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(genearray.get(i).synonymous); dot = true; } if (genearray.get(i).utr > 0) { if (dot) { buf.setColor(Color.white); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString(", ", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(", "); } buf.setColor(Color.lightGray); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString("" + genearray.get(i).utr, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(genearray.get(i).utr); dot = true; } if (genearray.get(i).intronic > 0) { if (dot) { buf.setColor(Color.white); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString(", ", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(", "); } buf.setColor(Color.gray); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString("" + genearray.get(i).intronic, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append(genearray.get(i).intronic); dot = true; } if (genearray.get(i).intergenic) { buf.setColor(Color.gray); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString("" + genearray.get(i).mutations, (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); mutcountbuffer.append("" + genearray.get(i).mutations); } buf.setColor(Color.white); textWidth = (int) fm.getStringBounds(mutcountbuffer.toString(), buf).getWidth(); buf.drawString(") ", (int) (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(); if (genearray.get(i).samples.size() == 1) { buf.drawString(" 1 sample", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString(" " + genearray.get(i).samples.size() + " samples", (int) (headerlengths[1][0]) + 5 + textWidth, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) (headerlengths[2][0]) + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (genearray.get(i).equals(hoverNode) || genearray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } if (genearray.get(i).intergenic) { if (genearray.get(i).varnodes.get(0).getTranscripts() == null) { buf.drawString(genearray.get(i).getChrom(), (int) (headerlengths[2][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (genearray.get(i).varnodes.get(0).getTranscripts().size() == 2) { buf.drawString( genearray.get(i).getChrom() + ":" + MethodLibrary.formatNumber(genearray.get(i).getEnd()) + "-" + MethodLibrary.formatNumber(genearray.get(i).varnodes.get(0) .getTranscripts().get(1).getStart()), (int) (headerlengths[2][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (genearray.get(i).varnodes.get(0).getPosition() < genearray.get(i).getStart()) { buf.drawString( genearray.get(i).getChrom() + ":1-" + MethodLibrary.formatNumber(genearray.get(i).varnodes.get(0) .getTranscripts().get(1).getStart()), (int) (headerlengths[2][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString( genearray.get(i).getChrom() + ":" + MethodLibrary.formatNumber(genearray.get(i).getEnd()) + "-end", (int) (headerlengths[2][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } else { buf.drawString( genearray.get(i).getChrom() + ":" + MethodLibrary.formatNumber(genearray.get(i).getStart()) + "-" + MethodLibrary.formatNumber(genearray.get(i).getEnd()), (int) (headerlengths[2][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) (headerlengths[3][0]) + 1, (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); if (genearray.get(i).equals(hoverNode) || genearray.get(i).equals(selectedNode)) { buf.setColor(Color.yellow); } else { buf.setColor(Color.white); } if (genearray.get(i).intergenic) { if (genearray.get(i).varnodes.get(0).getTranscripts() == null) { buf.drawString("-", (int) (headerlengths[3][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else if (genearray.get(i).varnodes.get(0).getTranscripts().size() == 2) { buf.drawString( genearray.get(i).getDescription() + ";" + genearray.get(i).varnodes.get(0).getTranscripts().get(1).getGene() .getDescription(), (int) (headerlengths[3][0]) + 5, (rowHeight * (i + 1 + genemutcount)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } else { buf.drawString(genearray.get(i).getDescription(), (int) (headerlengths[3][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((int) (headerlengths[r][0]), (rowHeight * (i + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) (headerlengths[r][0]), (rowHeight * (i + genemutcount + 2)) - tablescroll.getVerticalScrollBar().getValue() + 3); } if (selectedNode != null && selectedNode.equals(genearray.get(i))) { hoverSample = -1; genemutcount = aminoarray.size() + 1; listAdd = 1; // buf.drawLine(10, (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 (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; } buf.setColor(textcolor); 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); hoverSample = -1; if (aminoarray.get(s).getRow()[1].equals("1")) { 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(); hoverSampleNode = aminoarray.get(s).getNode().vars.get(v).getValue().get(0); hoverBase = aminoarray.get(s).getRow()[5]; break; } } } // hoverSample = -1; } 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; } 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); if (h == 3) { if (aminoarray.get(s).getRow()[5].length() == 1) { buf.drawString( Main.getBase.get(aminoarray.get(s).getNode().getRefBase()) + ">" + aminoarray.get(s).getRow()[5], (int) geneheader.get(h)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { buf.drawString(aminoarray.get(s).getRow()[5], (int) geneheader.get(h)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(4)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(4)[2], rowHeight - 1); buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[h], (int) geneheader.get(4)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } else { 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(5)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(5)[2], 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(5)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 2; casefreq = 2 / (double) (Main.varsamples * 2 - 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(5)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); if (Control.controlData.controlsOn) { cases = 1; casefreq = 1 / (double) (Main.varsamples * 2 - 1); } } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(6)[1] + 10, (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(6)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } else { //TODO piirra mustat boksit buf.setColor(Color.black); buf.fillRect((int) geneheader.get(5)[1] + 10, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth(), rowHeight - 1); 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])) { for (int j = 0; j < aminoarray.get(s).getNode().vars.get(v).getValue() .size(); j++) { if (aminoarray.get(s).getNode().vars.get(v).getValue() .get(j).alleles != null) { continue; } if (aminoarray.get(s).getNode().vars.get(v).getValue().get(j) .isHomozygous()) { cases += 2; } else { cases += 1; } } } } casefreq = cases / (double) (Main.varsamples * 2 - cases); } } buf.setColor(textcolor); buf.drawString(aminoarray.get(s).getRow()[4], (int) geneheader.get(7)[1] + 14, (rowHeight * (i + s + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); // buf.setColor(Color.black); 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, 5), (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 - controlarray[e].alleles)), 2) + " (p=" + MethodLibrary.round( 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++) { bedarray = MethodLibrary.makeTrackArray(aminoarray.get(a).getNode(), aminoarray.get(a).getRow()[5]); if (bedarray != null) { for (int b = 0; b < bedarray.length; b++) { buf.setColor(Color.black); if (b == bedarray.length - 1) { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, this.getWidth() - (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1], rowHeight - 1); } else { buf.fillRect( (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 12, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + 4, (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[2], rowHeight - 1); } buf.setColor(Color.white); if (bedarray[b] != null) { buf.drawString(bedarray[b].toString(), (int) geneheader.get(geneheaderlength + Control.controlData.fileArray.size() * 2 + b)[1] + 14, (rowHeight * (i + a + listAdd + 2)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } } } } /*if(c < header.size()-1-Main.bedCanvas.bedTrack.size()) { buf.setColor(Color.black); buf.fillRect((int)header.get(c+1)[1]+1, (rowHeight*(i+genemutcount+1))-tablescroll.getVerticalScrollBar().getValue()+4, (int)header.get(c)[2], rowHeight-1); }*/ // } buf.setColor(Color.darkGray); for (int j = 0; j < geneheader.size(); j++) { buf.drawLine((int) geneheader.get(j)[1] + 11, (rowHeight * (i + s + 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) { 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 (aminoarray.get(s).getNode().vars.get(v).getValue().get(l) .getSample().annotation) { continue; } 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(); hoverSampleNode = aminoarray.get(s).getNode().vars.get(v).getValue() .get(l); hoverBase = aminoarray.get(s).getRow()[5]; } 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(5)[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(5)[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(5)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); } buf.setColor(Color.black); buf.fillRect((int) geneheader.get(6)[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(6)[1] + 14, (rowHeight * (i + s + pointer + 3)) - tablescroll.getVerticalScrollBar().getValue() + rowHeight); buf.setColor(Color.darkGray); for (int j = 5; 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 * (genearray.size() + genemutcount + 1)) - tablescroll.getVerticalScrollBar().getValue() + 3, this.getWidth(), (rowHeight * (genearray.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); }
From source file:org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.java
/** * Implemented as specified by the {@link TreeViewer} interface. * @see TreeViewer#onDataObjectSave(DataObject, DataObject, int) *//*from w ww . j ava2 s. co m*/ public void onDataObjectSave(DataObject data, DataObject parent, int operation) { int state = model.getState(); if (operation == REMOVE_OBJECT && state != SAVE) throw new IllegalStateException("This method can only be " + "invoked in the SAVE state"); switch (state) { case DISCARDED: throw new IllegalStateException("This method cannot be " + "invoked in the DISCARDED state"); } if (data == null) throw new IllegalArgumentException("No data object. "); switch (operation) { case CREATE_OBJECT: case UPDATE_OBJECT: case REMOVE_OBJECT: break; default: throw new IllegalArgumentException("Save operation not " + "supported."); } //removeEditor(); //remove the currently selected editor. if (operation == REMOVE_OBJECT) { model.setState(READY); fireStateChange(); } view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); Browser browser = null; if (operation == CREATE_OBJECT) { if (parent == null) { if ((data instanceof ProjectData) || (data instanceof DatasetData)) browser = model.getBrowser(Browser.PROJECTS_EXPLORER); else if (data instanceof ScreenData) browser = model.getBrowser(Browser.SCREENS_EXPLORER); else if (data instanceof TagAnnotationData) browser = model.getBrowser(Browser.TAGS_EXPLORER); } if (browser != null) { model.setSelectedBrowser(browser); view.addBrowser(browser); removeEditor(); } } browser = model.getSelectedBrowser(); if (browser != null && operation != UPDATE_OBJECT) browser.refreshTree(null, null); if (operation == REMOVE_OBJECT || operation == CREATE_OBJECT) { DataBrowserFactory.discardAll(); view.removeAllFromWorkingPane(); } if (operation == UPDATE_OBJECT && browser != null) { browser.accept(new UpdateVisitor(browser, data)); browser.getUI().repaint(); } setStatus(false, "", true); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }
From source file:org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.java
/** * Implemented as specified by the {@link TreeViewer} interface. * @see TreeViewer#onOrphanDataObjectCreated(DataObject, int) *///w ww . j a v a2 s . c o m public void onOrphanDataObjectCreated(DataObject data) { view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); Browser browser = model.getSelectedBrowser(); if (browser != null) browser.onOrphanDataObjectCreated(data); setStatus(false, "", true); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }
From source file:pl.edu.icm.visnow.geometries.viewer3d.Display3DPanel.java
public void setPick3DActive(boolean pick3DActive) { if (!pick3DActive) { this.removeChild(pickObject.getOutObject()); setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); } else {/*from ww w . j a va 2s. c om*/ this.addChild(pickObject.getOutObject()); // setCursor(new Cursor(Cursor.CROSSHAIR_CURSOR)); // not needed? initializeOnceCrosshairCursor(); setCursor(crosshairCursor); } this.pickObject.setActive(pick3DActive); }
From source file:org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.java
/** * Implemented as specified by the {@link TreeViewer} interface. * @see TreeViewer#onDataObjectSave(List, int) *///from w w w .j a v a2 s. c om public void onDataObjectSave(List data, int operation) { int state = model.getState(); if (operation == REMOVE_OBJECT && state != SAVE) throw new IllegalStateException("This method can only be " + "invoked in the SAVE state"); switch (state) { case DISCARDED: throw new IllegalStateException("This method cannot be " + "invoked in the DISCARDED state"); } if (data == null) throw new IllegalArgumentException("No data object. "); switch (operation) { case CREATE_OBJECT: case UPDATE_OBJECT: case REMOVE_OBJECT: break; default: throw new IllegalArgumentException("Save operation not " + "supported."); } //removeEditor(); //remove the currently selected editor. if (operation == REMOVE_OBJECT) { model.setState(READY); fireStateChange(); } view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); setStatus(false, "", true); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }
From source file:org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.java
/** * Implemented as specified by the {@link TreeViewer} interface. * @see TreeViewer#clearFoundResults()//from w w w. j a v a 2s. c o m */ public void clearFoundResults() { switch (model.getState()) { case DISCARDED: case SAVE: return; } Browser browser = model.getSelectedBrowser(); view.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); if (browser != null) { browser.accept(new ClearVisitor()); browser.setFoundInBrowser(null); } view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); }
From source file:com.mirth.connect.client.ui.browsers.message.MessageBrowser.java
/** * An action for when a row is selected in the table *///from w w w . j a va2 s . c o m private void MessageListSelected(ListSelectionEvent evt) { if (!evt.getValueIsAdjusting()) { int row = getSelectedMessageIndex(); if (row >= 0) { // Cancel all pretty printing tasks for (Future<Void> worker : prettyPrintWorkers) { worker.cancel(true); } prettyPrintWorkers.clear(); parent.setVisibleTasks(parent.messageTasks, parent.messagePopupMenu, 6, 6, true); parent.setVisibleTasks(parent.messageTasks, parent.messagePopupMenu, 7, -1, isChannelDeployed); this.setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); // Get the table node MessageBrowserTableNode messageNode = (MessageBrowserTableNode) messageTreeTable.getPathForRow(row) .getLastPathComponent(); if (messageNode.isNodeActive()) { // Get the messageId from the message node Long messageId = messageNode.getMessageId(); // Get the metaDataId from the message node Integer metaDataId = messageNode.getMetaDataId(); // Attempt to get the message from the message cache Message message = messageCache.get(messageId); List<Attachment> attachments = attachmentCache.get(messageId); // If the message is not in the cache, retrieve it from the server if (message == null) { try { message = parent.mirthClient.getMessageContent(channelId, messageId, selectedMetaDataIds); // If the message was not found (ie. it may have been deleted during the request), do nothing if (message == null || message.getConnectorMessages().size() == 0) { clearDescription( "Could not retrieve message content. The message may have been deleted."); this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); return; } attachments = parent.mirthClient.getAttachmentsByMessageId(channelId, messageId, false); } catch (Throwable t) { if (t.getMessage().contains("Java heap space")) { parent.alertError(parent, "There was an out of memory error when trying to retrieve message content.\nIncrease your heap size and try again."); } else if (t instanceof RequestAbortedException) { // The client is no longer waiting for the message content request } else { parent.alertThrowable(parent, t); } this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); return; } // Add the retrieved message to the message cache messageCache.put(messageId, message); attachmentCache.put(messageId, attachments); } ConnectorMessage connectorMessage = message.getConnectorMessages().get(metaDataId); if (connectorMessage != null) { // Update the message tabs updateDescriptionMessages(connectorMessage); // Update the mappings tab updateDescriptionMappings(connectorMessage); // Update the attachments tab updateAttachmentsTable(messageId); // Update the errors tab updateDescriptionErrors(connectorMessage); // Show relevant tabs. Not using errorCode here just in case for some reason there are errors even though errorCode is 0 updateDescriptionTabs(connectorMessage.getProcessingError() != null || connectorMessage.getPostProcessorError() != null || connectorMessage.getResponseError() != null, attachments.size() > 0); updateMessageRadioGroup(); if (attachmentTable == null || attachmentTable.getSelectedRow() == -1 || descriptionTabbedPane.indexOfTab("Attachments") == -1) { parent.setVisibleTasks(parent.messageTasks, parent.messagePopupMenu, 9, 10, false); } } } else { clearDescription(null); } this.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); } } }
From source file:org.openmicroscopy.shoola.agents.treeviewer.view.TreeViewerComponent.java
/** * Implemented as specified by the {@link TreeViewer} interface. * @see TreeViewer#setExistingObjects(List) *//*from ww w . ja v a 2 s . c om*/ public void setExistingObjects(List objects) { if (model.getState() != LOADING_DATA) throw new IllegalStateException("This method cannot be invoked in the LOADING_DATA state."); setStatus(false, "", true); view.setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); model.setState(READY); if (CollectionUtils.isEmpty(objects)) return; Browser b = model.getSelectedBrowser(); List<Object> available = new ArrayList<Object>(); List<Object> immutable = new ArrayList<Object>(); Set selected = null; if (b != null) { TreeImageDisplay[] values = b.getSelectedDisplays(); if (values != null && values.length > 0) { // Only modify the first group from the list of groups Object value = values[0].getUserObject(); if (value instanceof GroupData) { long groupId = ((GroupData) value).getId(); ExperimenterData currentUser = model.getExperimenter(); selected = new HashSet<ExperimenterData>(); long userID = currentUser.getId(); long id; List<Long> ids = new ArrayList<Long>(); for (ExperimenterData experimenter : (List<ExperimenterData>) objects) { id = experimenter.getId(); if (experimenter.isMemberOfGroup(groupId)) { ids.add(id); selected.add(experimenter); //Cannot move guest or root if ((model.isSystemUser(id, GroupData.GUEST) && model.isSystemGroup(groupId, GroupData.GUEST))) { immutable.add(experimenter); } else if (model.isSystemGroup(groupId, GroupData.SYSTEM)) { if (model.isSystemUser(id, GroupData.SYSTEM) || id == userID) { immutable.add(experimenter); } } } if (!ids.contains(experimenter.getId())) { available.add(experimenter); } } } } else { available.addAll(objects); } } fireStateChange(); SelectionWizard d = new SelectionWizard(view, available, selected, objects.get(0).getClass(), TreeViewerAgent.getUserDetails()); d.setImmutableElements(immutable); IconManager icons = IconManager.getInstance(); String title = "User Selection"; String text = "Select the Users who should be in the selected group."; Icon icon = icons.getIcon(IconManager.OWNER_48); d.setTitle(title, text, icon); d.addPropertyChangeListener(controller); UIUtilities.centerAndShow(d); }
From source file:erigo.ctstream.CTstream.java
/** * //from ww w . j av a 2 s . c o m * mouseMoved * * Implement the mouseMoved method defined by interface MouseMotionListener. * * This method is part of our homemade window manager; specifically, this method * handles setting the appropriate mouse cursor based on where the user has * positioned the mouse on the JFrame window. * * Why have we implemented our own window manager? Since translucent panels * can only be contained within undecorated Frames (see comments in the top * header above) and since undecorated Frames don't support moving/resizing, * we implement our own basic "window manager" by catching mouse move and drag * events. * * @author John P. Wilson * @see java.awt.event.MouseMotionListener#mouseMoved(java.awt.event.MouseEvent) */ @Override public void mouseMoved(MouseEvent mouseEventI) { // System.err.println("mouseMoved: " + mouseEventI.getX() + "," + mouseEventI.getY()); mouseCommandMode = NO_COMMAND; // Set mouse Cursor based on the current mouse position int commandMode = getGUIFrameCommandMode(mouseEventI.getPoint()); switch (commandMode) { case NO_COMMAND: guiFrame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); break; case MOVE_FRAME: guiFrame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); break; case RESIZE_FRAME_NW: guiFrame.setCursor(new Cursor(Cursor.NW_RESIZE_CURSOR)); break; case RESIZE_FRAME_N: guiFrame.setCursor(new Cursor(Cursor.N_RESIZE_CURSOR)); break; case RESIZE_FRAME_NE: guiFrame.setCursor(new Cursor(Cursor.NE_RESIZE_CURSOR)); break; case RESIZE_FRAME_E: guiFrame.setCursor(new Cursor(Cursor.E_RESIZE_CURSOR)); break; case RESIZE_FRAME_SE: guiFrame.setCursor(new Cursor(Cursor.SE_RESIZE_CURSOR)); break; case RESIZE_FRAME_S: guiFrame.setCursor(new Cursor(Cursor.S_RESIZE_CURSOR)); break; case RESIZE_FRAME_SW: guiFrame.setCursor(new Cursor(Cursor.SW_RESIZE_CURSOR)); break; case RESIZE_FRAME_W: guiFrame.setCursor(new Cursor(Cursor.W_RESIZE_CURSOR)); break; default: guiFrame.setCursor(new Cursor(Cursor.DEFAULT_CURSOR)); break; } }
From source file:org.jab.docsearch.DocSearch.java
/** * Load properties file.//ww w. jav a2s .c o m * * @param propertiesFile * Properties file * @return Properties */ private Properties loadProperties(String propertiesFile) { logger.debug("loadProperties('" + propertiesFile + "') entered"); // cursor "wait" setCursor(Cursor.getPredefinedCursor(Cursor.WAIT_CURSOR)); // read property file Properties props = new Properties(); FileInputStream fileIn = null; try { File propsFile = new File(propertiesFile); if (propsFile.isFile()) { fileIn = new FileInputStream(propsFile); props.load(fileIn); } else { logger.error("loadProperties() " + propertiesFile + " isn't a file!"); } } catch (IOException ioe) { logger.fatal("loadProperties() failed", ioe); showMessage(dsErrLdgFi, "\n" + propertiesFile + "\n\n : " + ioe.toString()); } finally { IOUtils.closeQuietly(fileIn); } // cursor "default" setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); return props; }