List of usage examples for javax.swing JFileChooser setMultiSelectionEnabled
@BeanProperty(description = "Sets multiple file selection mode.") public void setMultiSelectionEnabled(boolean b)
From source file:org.eurocarbdb.application.glycoworkbench.plugin.s3.Cockpit.java
/** * Downloads the objects currently selected in the objects table. The user is * prompted/*from w w w . j a v a2 s.c o m*/ * Prepares to perform a download of objects from S3 by prompting the user for a directory * to store the files in, then performing the download. * * @throws IOException */ private void downloadSelectedObjects() { // Prompt user to choose directory location for downloaded files (or cancel download altogether) JFileChooser fileChooser = new JFileChooser(); fileChooser.setDialogTitle("Choose directory to save S3 files in"); fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); fileChooser.setMultiSelectionEnabled(false); fileChooser.setSelectedFile(downloadDirectory); int returnVal = fileChooser.showDialog(ownerFrame, "Choose Directory"); if (returnVal != JFileChooser.APPROVE_OPTION) { return; } downloadDirectory = fileChooser.getSelectedFile(); // Find clashing files final Map filesAlreadyInDownloadDirectoryMap = new HashMap(); S3Object[] objectsForDownload = getSelectedObjects(); for (int i = 0; i < objectsForDownload.length; i++) { File file = new File(downloadDirectory, objectsForDownload[i].getKey()); if (file.exists()) { filesAlreadyInDownloadDirectoryMap.put(objectsForDownload[i].getKey(), file); } } // Build map of S3 Objects being downloaded. final Map s3DownloadObjectsMap = FileComparer.getInstance().populateS3ObjectMap("", objectsForDownload); final HyperlinkActivatedListener hyperlinkListener = this; runInBackgroundThread(new Runnable() { public void run() { // Retrieve details of objects for download if (!retrieveObjectsDetails(getSelectedObjects())) { return; } try { final FileComparerResults comparisonResults = compareRemoteAndLocalFiles( filesAlreadyInDownloadDirectoryMap, s3DownloadObjectsMap); DownloadPackage[] downloadPackages = buildDownloadPackageList(comparisonResults, s3DownloadObjectsMap); if (downloadPackages == null) { return; } s3ServiceMulti.downloadObjects(currentSelectedBucket, downloadPackages); } catch (final Exception e) { runInDispatcherThreadImmediately(new Runnable() { public void run() { String message = "Unable to download objects"; log.error(message, e); ErrorDialog.showDialog(ownerFrame, hyperlinkListener, message, e); } }); } } }); }
From source file:org.fhaes.analysis.FHInterval.java
/** * Actually perform the analysis.//from w w w .ja va 2s .c o m */ @SuppressWarnings("deprecation") private void doAnalysis() { log.debug("INPUT PARAMETERS"); log.debug("inputFileArray = " + inputFileArray); log.debug("analyissType = " + analysisType); log.debug("startYear = " + startYear); log.debug("endYear = " + endYear); log.debug("fireFilterType = " + fireFilterType); log.debug("filterValue = " + filterValue); log.debug("includeIncomplete = " + includeIncomplete); log.debug("alphaLevel = " + alphaLevel); boolean highway = true; ArrayList<FHX2FileReader> myReader = new ArrayList<FHX2FileReader>(); Integer minFirstYear = new Integer(9999); Integer maxLastYear = new Integer(0); String savePath = new String(); savePath = inputFileArray[0].getAbsolutePath(); for (int i = 0; i < inputFileArray.length; i++) { myReader.add(new FHX2FileReader(inputFileArray[i])); /* * set the beginning year accounting for the filter */ if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_EVENT)) { // myReader.get(i).makeClimate2d(); if (startYear == 0 && highway) { if (myReader.get(i).getFirstFireYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstFireYear(); } } else if (startYear != 0 && highway) { if (myReader.get(i).getFirstYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstYear(); } } if (startYear != 0) { minFirstYear = startYear; // minFirstYear = minFirstYear+1; } } else if (eventTypeToProcess.equals(EventTypeToProcess.INJURY_EVENT)) { // myReader.get(i).makeClimate2dII(); if (startYear == 0 && highway) { if (myReader.get(i).getFirstInjuryYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstInjuryYear(); } } else if (startYear != 0 && highway) { if (myReader.get(i).getFirstYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstYear(); } } if (startYear != 0) { minFirstYear = startYear; // minFirstYear = minFirstYear+1; } } else if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_AND_INJURY_EVENT)) { // myReader.get(i).makeClimate2dII(); if (startYear == 0 && highway) { if (myReader.get(i).getFirstIndicatorYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstIndicatorYear(); } } else if (startYear != 0 && highway) { if (myReader.get(i).getFirstYear() < minFirstYear) { minFirstYear = myReader.get(i).getFirstYear(); } } if (startYear != 0) { minFirstYear = startYear; // minFirstYear = minFirstYear+1; } } else { log.error("Unsupported event type caught"); } /* * Set the last year accounting for the filter */ if (myReader.get(i).getLastYear() > maxLastYear) { maxLastYear = myReader.get(i).getLastYear(); } if (endYear != 0) { maxLastYear = endYear; } } // end of i loop log.debug("the input filelength is " + inputFileArray.length); log.debug("The FIRST FIRE YEAR is " + minFirstYear); log.debug("The LAST YEAR is " + maxLastYear); log.debug("Minimum and Maximum years are " + minFirstYear + " " + maxLastYear); /* * set the format for the output of the numbers to 2 decimal formats */ DecimalFormat twoPlace = new DecimalFormat("0.00"); DecimalFormat threePlace = new DecimalFormat("0.000"); /* * Calculate the listYears the common years where the files will be analyzed */ ArrayList<Integer> listYears = new ArrayList<Integer>(); for (int i = 0; i < maxLastYear - minFirstYear + 1; i++) { listYears.add(minFirstYear + i); } /* * create arraylist need for the Interval Analysis */ ArrayList<ArrayList<Integer>> climateMatrixSite = new ArrayList<ArrayList<Integer>>(); ArrayList<ArrayList<Double>> filterMatrix = new ArrayList<ArrayList<Double>>(); ArrayList<Integer> climateVector = new ArrayList<Integer>(); ArrayList<ArrayList<Double>> climateVectorFilter2 = new ArrayList<ArrayList<Double>>(); // ArrayList<Double> fireintervalspersite = new ArrayList<Double>(); ArrayList<Integer> climateVectorActualSite = null; ArrayList<Double> filterVectorActual = null; ArrayList<Integer> climateYear = new ArrayList<Integer>(); ArrayList<Integer> minSampleFilter = null; ArrayList<Double> percentOfRecordingfilter = null; Double[] Dfireintervalspersite; double[] dfireintervalspersite; String[] statsparam = new String[22]; if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_EVENT)) { statsparam[0] = "Total intervals"; statsparam[1] = "Mean fire interval"; statsparam[2] = "Median fire interval"; statsparam[3] = "Standard deviation"; statsparam[4] = "Fire frequency"; statsparam[5] = "Coefficient of variation"; statsparam[6] = "Skewness"; statsparam[7] = "Kurtosis"; statsparam[8] = "Minimum fire interval"; statsparam[9] = "Maximum fire interval"; statsparam[10] = "Weibull scale parameter"; statsparam[11] = "Weibull shape parameter"; statsparam[12] = "Weibull mean"; statsparam[13] = "Weibull median"; statsparam[14] = "Weibull mode"; statsparam[15] = "Weibull standard deviation"; statsparam[16] = "Weibull fire frequency"; statsparam[17] = "Weibull skewness"; statsparam[18] = "Lower exceedance interval"; statsparam[19] = "Upper exceedance interval"; statsparam[20] = "Significantly short interval upper bound"; statsparam[21] = "Significantly long interval lower bound"; } else if (eventTypeToProcess.equals(EventTypeToProcess.INJURY_EVENT)) { statsparam[0] = "Total intervals"; statsparam[1] = "Mean indicator interval"; statsparam[2] = "Median indicator interval"; statsparam[3] = "Standard deviation"; statsparam[4] = "Indicator frequency"; statsparam[5] = "Coefficient of variation"; statsparam[6] = "Skewness"; statsparam[7] = "Kurtosis"; statsparam[8] = "Minimum fire interval"; statsparam[9] = "Maximum indicator interval"; statsparam[10] = "Weibull scale parameter"; statsparam[11] = "Weibull shape parameter"; statsparam[12] = "Weibull mean"; statsparam[13] = "Weibull median"; statsparam[14] = "Weibull mode"; statsparam[15] = "Weibull standard deviation"; statsparam[16] = "Weibull indicator frequency"; statsparam[17] = "Weibull skewness"; statsparam[18] = "Lower exceedance interval"; statsparam[19] = "Upper exceedance interval"; statsparam[20] = "Significantly short interval upper bound"; statsparam[21] = "Significantly long interval lower bound"; } else if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_AND_INJURY_EVENT)) { statsparam[0] = "Total intervals"; statsparam[1] = "Mean fire and other indicator interval"; statsparam[2] = "Median fire and other indicator interval"; statsparam[3] = "Standard deviation"; statsparam[4] = "Fire and other indicator frequency"; statsparam[5] = "Coefficient of variation"; statsparam[6] = "Skewness"; statsparam[7] = "Kurtosis"; statsparam[8] = "Minimum fire and other indicator interval"; statsparam[9] = "Maximum fire interval"; statsparam[10] = "Weibull scale parameter"; statsparam[11] = "Weibull shape parameter"; statsparam[12] = "Weibull mean"; statsparam[13] = "Weibull median"; statsparam[14] = "Weibull mode"; statsparam[15] = "Weibull standard deviation"; statsparam[16] = "Weibull indicator frequency"; statsparam[17] = "Weibull skewness"; statsparam[18] = "Lower exceedance interval"; statsparam[19] = "Upper exceedance interval"; statsparam[20] = "Significantly short interval upper bound"; statsparam[21] = "Significantly long interval lower bound"; } else { log.error("Unsupported event type caught"); } double[] fixvalt = { 0.999, 0.99, 0.975, 0.95, 0.9, 0.875, 0.8, 0.75, 0.7, 0.667, 0.5, 0.333, 0.3, 0.25, 0.2, 0.125, 0.1, 0.05, 0.025, 0.01, 0.001 }; double[][] ExceeProbcomp = new double[fixvalt.length][myReader.size()]; double[][] ExceeProbsample = new double[fixvalt.length][myReader.size()]; // log.debug("the size of statsparam is " + // statsparam.length); double[][] summaryComp = new double[statsparam.length][myReader.size()]; double[] numberOfintervalscomp = new double[myReader.size()]; // ArrayList<ArrayList<Integer>>(); // ArrayList<ArrayList<Integer>> FIyearperSample = new // ArrayList<ArrayList<Integer>>(); ArrayList<Integer> FyearperSampletemp; ArrayList<Integer> FIyearperSampletemp; // ArrayList<Double> fireintervalspersample = new double[] numberOfintervalssamp = new double[myReader.size()]; double[][] summarySample = new double[statsparam.length][myReader.size()]; Double[] Dfireintervalspersample; double[] dfireintervalspersample; /* * Set up either of the two filters two create the binary matrix on the case of composite analysis there are two possible filters: * Number of fires and percentage of scarred trees. */ Integer firesFilter1 = new Integer(0); Double firesFilter2 = new Double(0); if (fireFilterType.equals(FireFilterType.NUMBER_OF_EVENTS)) { if (filterValue != 1) firesFilter1 = filterValue.intValue(); // log.debug("number of fires is selected is: "+ // firesFilter1); } else if (fireFilterType.equals(FireFilterType.PERCENTAGE_OF_ALL_TREES)) { if (filterValue != 1) firesFilter2 = filterValue / 100.0; // log.debug("percentage of fires is selected is: "+ // firesFilter2); } else if (fireFilterType.equals(FireFilterType.PERCENTAGE_OF_RECORDING)) { if (filterValue != 1) firesFilter2 = filterValue / 100.0; // TODO ELENA TO CHECK } else { log.error("Unknown FireFilterType"); return; } boolean[] enoughIntComp = new boolean[myReader.size()]; boolean[] enoughIntSamp = new boolean[myReader.size()]; // NEW FOR ELENA log.debug("Sample depth filter type = " + sampleDepthFilterType); log.debug("Sample depth value = " + sampleDepthFilterValue); // if (sampleDepthFilterType.equals(SampleDepthFilterType.MIN_NUM_SAMPLES)) // { // // TODO ELENA // } // else if (sampleDepthFilterType.equals(SampleDepthFilterType.MIN_NUM_RECORDER_SAMPLES)) // { // // TODO ELENA // } /* * start processing each file individually: The analysis can be done by either tree (by sample/non-binary) or by site * (composite/binary). by tree the box selected is: jCheckTree. by site the box selected is: */ for (int i = 0; i < myReader.size(); i++) { log.debug(" Starting to Process file : " + myReader.get(i).getName()); /* * get the vector Year containing the vector of year of a given fhx file load it into the array list climateYear. */ climateYear = myReader.get(i).getYearArray(); // new stuff // Create filter based on min number of samples/recorder samples int[] depths = null; if (sampleDepthFilterType.equals(SampleDepthFilterType.MIN_NUM_SAMPLES)) { depths = myReader.get(i).getSampleDepths(); log.debug("MIN_NUM_SAMPLES "); } else if (sampleDepthFilterType.equals(SampleDepthFilterType.MIN_NUM_RECORDER_SAMPLES)) { depths = myReader.get(i).getRecordingDepths(eventTypeToProcess); log.debug(" MIN_NUM_RECORDER_SAMPLES"); } else { log.error("Unknown sample depth filter type."); return; } minSampleFilter = new ArrayList<Integer>(); for (int ij = 0; ij < listYears.size(); ij++) { if (climateYear.indexOf(listYears.get(ij)) == -1) { minSampleFilter.add(-1); } else { // log.debug("the sample depth is " // + myReader.get(i).getSampleDepths()[climateYear.indexOf(listYearsComp.get(ij))]); minSampleFilter.add(new Integer(depths[climateYear.indexOf(listYears.get(ij))])); } // log.debug(" " + minSampleFilter.get(ij)); } // end new stuff /* * get filter matrix for each file. * * filters2d matrix composed of the 3 filters number of fires (total capital letter per row) total number of tree (total lower * case letter plus bars counting only after a fire) percent of scared trees total fires/total trees */ // climateVectorFilter2 = myReader.get(i).getFilterArrays(eventTypeToProcess); /* * More new stuff */ if (filterValue != 1) { /* * get both matrices: * * 2. filters2d matrix composed of the 3 filters number of fires (total capital letter per row) total number of tree (total * lower case letter plus bars counting only after a fire) percent of scared trees total fires/total trees */ climateVectorFilter2 = myReader.get(i).getFilterArrays(eventTypeToProcess); /* * if by tree analysis is selected create two matrices (array list) 1. filterMatrix containing the three filter vectors only * in between common years (so using the listYearComp array list subset of the years vector) 2. climateMatrix 2 dimensional * array list containing binary matrices restricted to the listYear list. */ if (fireFilterType.equals(FireFilterType.PERCENTAGE_OF_RECORDING)) { percentOfRecordingfilter = new ArrayList<Double>(); for (int ij = 0; ij < listYears.size(); ij++) { if (climateYear.indexOf(listYears.get(ij)) == -1) { percentOfRecordingfilter.add(-1.0); } else { if (myReader.get(i).getRecordingDepths(eventTypeToProcess)[climateYear .indexOf(listYears.get(ij))] != 0) { percentOfRecordingfilter.add(new Double( climateVectorFilter2.get(0).get(climateYear.indexOf(listYears.get(ij))) / myReader.get(i).getRecordingDepths(eventTypeToProcess)[climateYear .indexOf(listYears.get(ij))])); } else { percentOfRecordingfilter.add(-99.0); } } log.debug("PERCENTAGE_OF_RECORDING is: " + percentOfRecordingfilter.get(ij)); } } else { for (int ik = 0; ik < 3; ik++) { log.debug("filter number is: " + ik); filterVectorActual = new ArrayList<Double>(); for (int ij = 0; ij < listYears.size(); ij++) { // log.debug(" climateYear.indexOf(listYearsComp.get(j))" + // climateYear.indexOf(listYearsComp.get(ij))); // if(ik==0){log.debug("number of fires // "+climateVectorFilter2.get(0).get(climateYear.indexOf(listYears.get(ij)))+" year // "+listYearsComp.get(ij));} if (climateYear.indexOf(listYears.get(ij)) == -1) { filterVectorActual.add(-1.0); } else { filterVectorActual.add(new Double( climateVectorFilter2.get(ik).get(climateYear.indexOf(listYears.get(ij))))); } if (ik == 2) { log.debug("filteperc " + filterVectorActual.get(ij)); } } // log.debug("size of filterVectorActual is : "+filterVectorActual.size()); filterMatrix.add(filterVectorActual); // if(ik==0){log.debug("filters is: "+filter); } } // end of if-else percentageofrecording // log.debug("size of the FilterMatrix is" + filterMatrix.size()); } // end of if filters not equal to 1 /* * end of more new stuff */ /* * * 1. Create the filterMatrix containing the tree filter vectors only in between common years (so using the listYearComp array * list subset of the years vector) */ // for (int ik = 0; ik < 3; ik++) // { // filterVectorActual = new ArrayList<Double>(); // for (int ij = 0; ij < listYears.size(); ij++) // { // if (climateYear.indexOf(listYears.get(ij)) == -1) // { // filterVectorActual.add(-1.0); // } // else // { // filterVectorActual.add(new Double(climateVectorFilter2.get(ik).get(climateYear.indexOf(listYears.get(ij))))); // } // } /* * ArrayList filterMatrix containes the filter matrix for each of the files */ // filterMatrix.add(filterVectorActual); // }//end of creating the filter matrix. /* * get matrix climate binary matrix by site (binary analysis) if Composite is selected. */ // if ((doComposite)&&(!jTextOfFires.getText().equals("1"))){ if (analysisType.equals(AnalysisType.COMPOSITE)) { log.debug("inside the comp"); // System.out.println("inside the comp " + " working on file "+ myReader.get(i).getName() ); if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_EVENT)) { climateVector = myReader.get(i).getFireEventsArray(); } else if (eventTypeToProcess.equals(EventTypeToProcess.INJURY_EVENT)) { climateVector = myReader.get(i).getOtherInjuriesArray(); } else if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_AND_INJURY_EVENT)) { climateVector = myReader.get(i).getFiresAndInjuriesArray(); } else { log.error("Unsupported event type caught"); } climateVectorActualSite = new ArrayList<Integer>(); for (int j = 0; j < listYears.size(); j++) { if (climateYear.indexOf(listYears.get(j)) == -1) { climateVectorActualSite.add(-1); } else { if (minSampleFilter.get(j).intValue() >= sampleDepthFilterValue.intValue()) { if (filterValue != 1) { if (fireFilterType.equals(FireFilterType.NUMBER_OF_EVENTS)) { // log.debug("fire filter: "+firesFilter1+" year is: "+listYears.get(j) // +" fires: "+filterMatrix.get(3*i).get(j)+" climatevector: // "+climateVector.get(climateYear.indexOf(listYears.get(j)))); if ((filterMatrix.get(3 * i).get(j) < firesFilter1) && (climateVector.get(climateYear.indexOf(listYears.get(j)))) != -1.0) { climateVectorActualSite.add(0); } else { climateVectorActualSite .add(climateVector.get(climateYear.indexOf(listYears.get(j)))); } } else if (fireFilterType.equals(FireFilterType.PERCENTAGE_OF_ALL_TREES)) { // log.debug("percent of fires is selected is: "+ // firesFilter2+" "+climateVector.get(climateYear.indexOf(listYearsComp.get(j)))); // log.debug("the filter percent of fires is"+filterMatrix.get((3*i+2)).get(j)); if ((filterMatrix.get(3 * i + 2).get(j) == -99)) { climateVectorActualSite.add(-1); } else { if ((filterMatrix.get(3 * i + 2).get(j) < firesFilter2) && ((climateVector .get(climateYear.indexOf(listYears.get(j)))) != -1.0)) { climateVectorActualSite.add(0); } else { climateVectorActualSite .add(climateVector.get(climateYear.indexOf(listYears.get(j)))); } } } else if (fireFilterType.equals(FireFilterType.PERCENTAGE_OF_RECORDING)) { // TODO // ELENA TO IMPLEMENT if (percentOfRecordingfilter.get(j) == -99) { climateVectorActualSite.add(-1); } else { if ((percentOfRecordingfilter.get(j) < firesFilter2) && ((climateVector .get(climateYear.indexOf(listYears.get(j)))) != -1.0)) { climateVectorActualSite.add(0); } else { climateVectorActualSite .add(climateVector.get(climateYear.indexOf(listYears.get(j)))); } } } else { log.error("Unknown FireFilterType"); return; } } // end of if filter not equal to 1 else { climateVectorActualSite .add(climateVector.get(climateYear.indexOf(listYears.get(j)))); } // end of else of if filter not equal to 1 } // end of if the filter minsampedepth else { // log.debug("j is " + j + "minSampleFilter is " + minSampleFilter.get(j)); climateVectorActualSite.add(-1); } } // end else 645 to 721 } // end of j loop listyears (420-459) /* * climateMatrixSite has the composite information taking in consideration both the filters and common years */ climateMatrixSite.add(climateVectorActualSite); /* * Must get the years with Fires from the climateMatrixSite which has been filter already */ ArrayList<Double> fireintervalspersite = new ArrayList<Double>(); ArrayList<Integer> yearsWithFires = new ArrayList<Integer>(); for (int ij = 0; ij < listYears.size(); ij++) { if (climateMatrixSite.get(i).get(ij) == 1) { yearsWithFires.add(listYears.get(ij)); log.debug("year with fires " + listYears.get(ij)); } } /* * check that the number of years with fires is bigger of equal than 3 if so make the fire intervals else the test can not * be run and report NA */ // new swich if (yearsWithFires.size() != 0) { if (includeIncomplete) { if (maxLastYear.compareTo(yearsWithFires.get(yearsWithFires.size() - 1)) != 0) { log.debug("here"); numberOfintervalscomp[i] = yearsWithFires.size(); } else { numberOfintervalscomp[i] = yearsWithFires.size() - 1; } } else { numberOfintervalscomp[i] = yearsWithFires.size() - 1; } } log.debug("number of invervlas in comp is: " + numberOfintervalscomp[i]); // end of new switch if (numberOfintervalscomp[i] >= 3) { enoughIntComp[i] = true; ArrayList<Integer> fireIntervals = generateFireIntervals(yearsWithFires); for (int ij = 0; ij < fireIntervals.size(); ij++) { // log.debug("fire intervals are: "+ // test1.getFireIntervals().get(ij)); fireintervalspersite.add(fireIntervals.get(ij) * 1.0); } /* * Add extra interval if include incomplete is selected. the interval goes from the last fire scar year to the last year * of the fire history. */ if (includeIncomplete) { double includeinterval = maxLastYear - yearsWithFires.get(yearsWithFires.size() - 1); if (includeinterval > 0) { fireintervalspersite.add(includeinterval); System.out.println("the last year is " + maxLastYear + "the last year with fire is " + yearsWithFires.get(yearsWithFires.size() - 1)); log.debug("the included interval is " + includeinterval); } } log.debug("FireintervalsPerSite =" + fireintervalspersite); /* * Get the normal statistics for the fire intervals add the values to the stats and then call them for the stats */ DescriptiveStatistics stats = new DescriptiveStatistics(); Dfireintervalspersite = new Double[fireintervalspersite.size()]; Dfireintervalspersite = fireintervalspersite.toArray(Dfireintervalspersite); dfireintervalspersite = new double[fireintervalspersite.size()]; // summaryComp = new // double[statsparam.length][myReader.size()]; for (int ik = 0; ik < fireintervalspersite.size(); ik++) { stats.addValue(Dfireintervalspersite[ik].doubleValue()); dfireintervalspersite[ik] = Dfireintervalspersite[ik].doubleValue(); } /* * load the Summary Analysis for the Composite fire intervals */ summaryComp[0][i] = fireintervalspersite.size(); // double mean = stats.getMean(); summaryComp[1][i] = stats.getMean(); // double median = // StatUtils.percentile(dfireintervalspersite, 50); summaryComp[2][i] = StatUtils.percentile(dfireintervalspersite, 50); // double std = stats.getStandardDeviation(); summaryComp[3][i] = stats.getStandardDeviation(); // double skew = stats.getSkewness(); summaryComp[4][i] = 1.0 / summaryComp[1][i]; summaryComp[5][i] = summaryComp[3][i] / summaryComp[1][i]; summaryComp[6][i] = stats.getSkewness(); // double kurt = stats.getKurtosis(); if (numberOfintervalscomp[i] == 3) { summaryComp[7][i] = -99; } else { summaryComp[7][i] = stats.getKurtosis(); } // log.debug("nomean \t\t nostd \t\t nokurt \t noskew \t\t nomedian"); // log.debug(twoPlace.format(mean)+"\t\t"+twoPlace.format(std)+"\t\t"+twoPlace.format(kurt)+"\t\t"+twoPlace.format(skew)+"\t\t"+twoPlace.format(median)); Weibull weibull = new Weibull(fireintervalspersite); ArrayList<Double> weibullProb = weibull.getWeibullProbability(fireintervalspersite); ArrayList<Double> siglonglowbound = new ArrayList<Double>(); ArrayList<Double> sigshortupbound = new ArrayList<Double>(); log.debug("the weibull probability of first element is " + weibullProb.get(0)); log.debug("the index the size of the interval is " + weibullProb.indexOf(weibullProb.get(0))); for (int ij = 0; ij < weibullProb.size() - 1; ij++) { if (weibullProb.get(ij) <= alphaLevel) { siglonglowbound.add(fireintervalspersite.get(ij)); } if (weibullProb.get(ij) >= (1 - alphaLevel)) { sigshortupbound.add(fireintervalspersite.get(ij)); } } summaryComp[10][i] = weibull.getScale(); summaryComp[11][i] = weibull.getShape(); summaryComp[12][i] = weibull.getMean(); summaryComp[13][i] = weibull.getMedian(); summaryComp[14][i] = weibull.getMode(); summaryComp[15][i] = weibull.getSigma(); summaryComp[16][i] = 1.0 / summaryComp[13][i]; summaryComp[17][i] = weibull.getSkew(); summaryComp[18][i] = weibull.getExceedenceProbability2()[0]; summaryComp[19][i] = weibull.getExceedenceProbability2()[1]; Collections.sort(sigshortupbound); log.debug("siglonglowbound is " + siglonglowbound); try { summaryComp[20][i] = sigshortupbound.get(sigshortupbound.size() - 1); } catch (Exception e) { summaryComp[20][i] = Double.NaN; } Collections.sort(siglonglowbound); try { summaryComp[21][i] = siglonglowbound.get(0); } catch (Exception e) { summaryComp[21][i] = Double.NaN; } log.debug("sigshortupbound is " + sigshortupbound); Collections.sort(fireintervalspersite); summaryComp[8][i] = fireintervalspersite.get(0); summaryComp[9][i] = fireintervalspersite.get(fireintervalspersite.size() - 1); // log.debug("shape \t\t scale \t\t median "); // log.debug(twoPlace.format(test1.Weibull_Parameters(fireintervalspersite)[0])+"\t\t"+twoPlace.format(test1.Weibull_Parameters(fireintervalspersite)[1])+"\t\t"+twoPlace.format(test1.weibull_median(test1.Weibull_Parameters(fireintervalspersite)))); // log.debug("mean \t\t sigma \t\t mode \t\t skewness"); // log.debug(twoPlace.format(test1.weibull_mean(test1.Weibull_Parameters(fireintervalspersite)))+"\t\t"+twoPlace.format(test1.weibull_sigma(test1.Weibull_Parameters(fireintervalspersite)))+"\t\t"+twoPlace.format(test1.weibull_mode(test1.Weibull_Parameters(fireintervalspersite)))+"\t\t"+twoPlace.format(test1.weibull_skew(test1.Weibull_Parameters(fireintervalspersite)))); // log.debug("maxhazard \t\t lei \t\t uei "); // log.debug(twoPlace.format(test1.maxhazard_int(test1.Weibull_Parameters(fireintervalspersite)))+"\t\t"+twoPlace.format(test1.weibull_lowuppexcint(test1.Weibull_Parameters(fireintervalspersite))[0])+"\t\t"+twoPlace.format(test1.weibull_lowuppexcint(test1.Weibull_Parameters(fireintervalspersite))[1])); // log.debug("the size of YearWith Fires is "+YearsWithFires.size()); System.out.println("the size of the prb exdc is " + weibull.getExceedenceProbability().length); for (int kk = 0; kk < weibull.getExceedenceProbability().length; kk++) { ExceeProbcomp[kk][i] = weibull.getExceedenceProbability()[kk]; // log.debug("file "+i+"Exce probability "+ // ExceeProbcomp[kk][i]); } } // end of if enoughIntComp else { enoughIntComp[i] = false; } } // end the if composite is selected /* * starting the process for the sample mode. */ if (analysisType.equals(AnalysisType.SAMPLE)) { log.debug("I am in sample "); ArrayList<Double> fireintervalspersample = new ArrayList<Double>(); FIyearperSampletemp = new ArrayList<Integer>(); // FyearperSampletemp = new ArrayList<Integer>(); for (int k = 0; k < myReader.get(i).getNumberOfSeries(); k++) { log.debug("Parsing file index " + i + ", series number " + (k + 1)); FyearperSampletemp = new ArrayList<Integer>(); // log.debug("the size of the years of the file is:"+ // myReader.get(i).getYear().size()); // log.debug("years with fires in sample "+k + // "years are "); // for (int j = 0; j < myReader.get(i).getYearArray().size(); j++) for (int j = 0; j < listYears.size(); j++) { // log.debug("the size climate2d is "+myReader.get(i).getClimate2d().get(k).get(j)); if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_EVENT)) { if (climateYear.indexOf(listYears.get(j)) != -1) { if (myReader.get(i).getClimate2d().get(k) .get(climateYear.indexOf(listYears.get(j))) == 1) { // FyearperSampletemp.add((j + myReader.get(i).getFirstYear())); FyearperSampletemp.add(listYears.get(j)); } } } // { // if ((myReader.get(i).getClimate2d().get(k).get(j) == 1)) // { // / log.debug("I here inside ==1 "+ // / j+" "+myReader.get(i).getFirstYear()); // / int temp=j+myReader.get(i).getFirstYear(); // / log.debug((j+myReader.get(i).getFirstYear())); // /// FyearperSampletemp.add((j + myReader.get(i).getFirstYear())); // } // } else if (eventTypeToProcess.equals(EventTypeToProcess.INJURY_EVENT)) { if (climateYear.indexOf(listYears.get(j)) != -1) { if (myReader.get(i).getClimate2dII().get(k) .get(climateYear.indexOf(listYears.get(j))) == 1) { FyearperSampletemp.add(listYears.get(j)); } } // if ((myReader.get(i).getClimate2dII().get(k).get(j) == 1)) // { // FyearperSampletemp.add((j + myReader.get(i).getFirstYear())); // } } else if (eventTypeToProcess.equals(EventTypeToProcess.FIRE_AND_INJURY_EVENT)) { if (climateYear.indexOf(listYears.get(j)) != -1) { if (myReader.get(i).getClimate2dIII().get(k) .get(climateYear.indexOf(listYears.get(j))) == 1) { FyearperSampletemp.add(listYears.get(j)); } } // if ((myReader.get(i).getClimate2dIII().get(k).get(j) == 1)) // { // FyearperSampletemp.add((j + myReader.get(i).getFirstYear())); // } } else { log.error("Unsupported event type caught"); } } // / end of the loop for listYears in common (finish loading the fire year per sample log.debug( "series number " + (k + 1) + " FyearperSampletemp.size() " + FyearperSampletemp.size()); if (FyearperSampletemp.size() != 0) { if (includeIncomplete) { if (maxLastYear.compareTo(FyearperSampletemp.get(FyearperSampletemp.size() - 1)) != 0) { numberOfintervalssamp[i] = numberOfintervalssamp[i] + FyearperSampletemp.size(); } } else { numberOfintervalssamp[i] = numberOfintervalssamp[i] + (FyearperSampletemp.size() - 1); } } log.debug("series number: " + (k + 1) + " number of intervals " + numberOfintervalssamp[i]); // new if ((FyearperSampletemp.size() == 1) && (includeIncomplete)) { log.debug("last index per sample is " + myReader.get(i).getLastYearIndexPerSample()[k]); log.debug("first year per sample is " + myReader.get(i).getFirstYear()); log.debug("maxLastyear is " + maxLastYear); // if (maxLastYear != FyearperSampletemp.get(FyearperSampletemp.size() - 1)) if (maxLastYear.compareTo(FyearperSampletemp.get(FyearperSampletemp.size() - 1)) != 0) { log.debug("I am in not equal "); log.debug( "last year in the sample is " + (myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear())); log.debug("maxLastyear is " + maxLastYear); log.debug("the last fire year in the sample " + FyearperSampletemp.get(FyearperSampletemp.size() - 1)); if (maxLastYear <= (myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear())) { Integer temp = ((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); // int temp1 = maxLastYear.intValue() - FyearperSampletemp.get(FyearperSampletemp.size() - 1).intValue(); log.debug("in less than or equal to "); // temp = (maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1); log.debug("the resta temp is " + temp); // FIyearperSampletemp.add(((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1))); if ((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1) > 0) { FIyearperSampletemp.add( (maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); log.debug("the fire intervals for sample " + k + " is " + FIyearperSampletemp.get(0)); } // FIyearperSampletemp.add(temp); // log.debug("the fire intervals for sample " + k + " is " + FIyearperSampletemp.get(0)); } else { log.debug("in else "); FIyearperSampletemp.add((myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear()) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); log.debug("fire intervals for sample " + k + " is " + FIyearperSampletemp.get(0)); } // FIyearperSampletemp.add((myReader.get(i).getFirstYear() + myReader.get(i).getLastYearIndexPerSample()[k]) // - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); } // log.debug("fire intervals for sample " + k + " is " + FIyearperSampletemp.get(0)); } // end of if one fire year and includelastyear so we have at least one interval in a given series. // endofnew if ((FyearperSampletemp.size() >= 2)) { log.debug("Series number is " + (k + 1)); for (int jk = 0; jk < FyearperSampletemp.size() - 1; jk++) { // FIyearperSampletemp.add(FyearperSample.get(k).get(jk+1) // - FyearperSample.get(k).get(jk)); log.debug("FyearperSampletemp is " + FyearperSampletemp.get(jk)); if ((FyearperSampletemp.get(jk + 1) - FyearperSampletemp.get(jk)) > 0) { FIyearperSampletemp .add(FyearperSampletemp.get(jk + 1) - FyearperSampletemp.get(jk)); } // FIyearperSampletemp.add(FyearperSampletemp.get(jk+1) // - FyearperSampletemp.get(jk)); log.debug("fire intervals for sample " + k + " is " + FIyearperSampletemp.get(jk)); // fisumtemp= fisumtemp + // FIyearperSampletemp.get(jk).intValue(); } if (includeIncomplete) { // if (maxLastYear != FyearperSampletemp.get(FyearperSampletemp.size() - 1)) if (maxLastYear.compareTo(FyearperSampletemp.get(FyearperSampletemp.size() - 1)) != 0) // if ((myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear()) != FyearperSampletemp // .get(FyearperSampletemp.size() - 1)) { if (maxLastYear <= (myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear())) { if (((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)) > 0) { FIyearperSampletemp.add(((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1))); } } else { FIyearperSampletemp.add((myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear()) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); } // log.debug("the sample number is "+k+ // " the size of the fyearpersampletemp is "+ // FyearperSampletemp.size() ); // log.debug("the last year per sample is " // + (myReader.get(i).getLastYearIndexPerSample()[k] + myReader.get(i).getFirstYear())); // log.debug(" the last fire year per sample " + FyearperSampletemp.get(FyearperSampletemp.size() - 1)); // FIyearperSampletemp.add((maxLastYear) - FyearperSampletemp.get(FyearperSampletemp.size() - 1)); // log.debug("the last intrval in included is on is " // + FIyearperSampletemp.get(FIyearperSampletemp.size() - 1)); } } } // end of if at least 2 fier years so we have at least one interval in a given series. log.debug("size of FIyearperSampletemp " + FIyearperSampletemp.size() + " at series is :" + (k + 1)); // FIyearperSampletemp.size()+ // " X "+FIyearperSampletemp.get(0).size()); } // end of the loop for number of series. // log.debug("size of FIyearperSample "+ // FIyearperSampletemp.size()); for (int j = 0; j < FIyearperSampletemp.size(); j++) { fireintervalspersample.add(FIyearperSampletemp.get(j) * 1.0); } /* * Get the normal statistics for the fire intervals add the values to the stats and then call them for the stats */ if (fireintervalspersample.size() >= 3) { enoughIntSamp[i] = true; DescriptiveStatistics stasample = new DescriptiveStatistics(); Dfireintervalspersample = new Double[fireintervalspersample.size()]; Dfireintervalspersample = fireintervalspersample.toArray(Dfireintervalspersample); dfireintervalspersample = new double[fireintervalspersample.size()]; // summarySample = new // double[statsparam.length][myReader.size()]; for (int ik = 0; ik < fireintervalspersample.size(); ik++) { stasample.addValue(Dfireintervalspersample[ik].doubleValue()); dfireintervalspersample[ik] = Dfireintervalspersample[ik].doubleValue(); log.debug("the " + ik + " fire interval is " + dfireintervalspersample[ik]); } log.debug("the size for dfireintervalspersample is " + dfireintervalspersample.length); // ADDED BY PETE if (dfireintervalspersample.length == 0) continue; /* * load the Summary Analysis for the Sample fire intervals */ summarySample[0][i] = fireintervalspersample.size(); // double mean = stats.getMean(); summarySample[1][i] = stasample.getMean(); log.debug("mean sample is " + stasample.getMean()); // double median = // StatUtils.percentile(dfireintervalspersite, 50); summarySample[2][i] = StatUtils.percentile(dfireintervalspersample, 50); log.debug("summarySample[2][] " + i + " " + summarySample[2][i]); // double std = stats.getStandardDeviation(); summarySample[3][i] = stasample.getStandardDeviation(); log.debug("summarySample[3][] " + i + " " + summarySample[3][i]); // double skew = stats.getSkewness(); summarySample[4][i] = 1.0 / summarySample[1][i]; log.debug("summarySample[4][] " + i + " " + summarySample[4][i]); summarySample[5][i] = summarySample[3][i] / summarySample[1][i]; log.debug("summarySample[5][] " + i + " " + summarySample[5][i]); summarySample[6][i] = stasample.getSkewness(); log.debug("summarySample[6][] " + i + " " + summarySample[6][i]); // double kurt = stats.getKurtosis(); if (numberOfintervalssamp[i] == 3) { summarySample[7][i] = -99; } else { summarySample[7][i] = stasample.getKurtosis(); } // summarySample[7][i] = stasample.getKurtosis(); log.debug("summarySample[7][] " + i + " " + summarySample[7][i]); // log.debug("nomean \t\t nostd \t\t nokurt \t noskew \t\t nomedian"); // log.debug(twoPlace.format(mean)+"\t\t"+twoPlace.format(std)+"\t\t"+twoPlace.format(kurt)+"\t\t"+twoPlace.format(skew)+"\t\t"+twoPlace.format(median)); Weibull weibull = new Weibull(fireintervalspersample); // ArrayList<Double> weibullProb = weibull.getWeibullProbability(fireintervalspersample); ArrayList<Double> siglonglowbound = new ArrayList<Double>(); ArrayList<Double> sigshortupbound = new ArrayList<Double>(); log.debug("the weibull probability of first element is " + weibullProb.get(0)); log.debug("the index the size of the interval is " + weibullProb.indexOf(weibullProb.get(0))); for (int ij = 0; ij < weibullProb.size() - 1; ij++) { if (weibullProb.get(ij) <= alphaLevel) { siglonglowbound.add(fireintervalspersample.get(ij)); } if (weibullProb.get(ij) >= (1 - alphaLevel)) { sigshortupbound.add(fireintervalspersample.get(ij)); } } // summarySample[10][i] = weibull.getScale(); log.debug("summarySample[10][] " + i + " " + summarySample[10][i]); summarySample[11][i] = weibull.getShape(); log.debug("summarySample[11][] " + i + " " + summarySample[11][i]); summarySample[12][i] = weibull.getMean(); summarySample[13][i] = weibull.getMedian(); summarySample[14][i] = weibull.getMode(); summarySample[15][i] = weibull.getSigma(); summarySample[16][i] = 1.0 / summarySample[13][i]; summarySample[17][i] = weibull.getSkew(); summarySample[18][i] = weibull.getExceedenceProbability2()[0]; summarySample[19][i] = weibull.getExceedenceProbability2()[1]; Collections.sort(sigshortupbound); log.debug("siglonglowbound is " + siglonglowbound); try { summarySample[20][i] = sigshortupbound.get(sigshortupbound.size() - 1); } catch (Exception e) { summarySample[20][i] = Double.NaN; } Collections.sort(siglonglowbound); try { summarySample[21][i] = siglonglowbound.get(0); } catch (Exception e) { summarySample[21][i] = Double.NaN; } log.debug("sigshortupbound is " + sigshortupbound); Collections.sort(fireintervalspersample); try { summarySample[8][i] = fireintervalspersample.get(0); } catch (Exception ex) { log.error("Index out of bounds exception caught: "); log.error(" summarySample[8][i] = fireintervalspersample.get(0)"); ex.printStackTrace(); } summarySample[9][i] = fireintervalspersample.get(fireintervalspersample.size() - 1); // log.debug("shape \t\t scale \t\t median "); // log.debug(twoPlace.format(test2.Weibull_Parameters(fireintervalspersample)[0])+"\t\t"+twoPlace.format(test2.Weibull_Parameters(fireintervalspersample)[1])+"\t\t"+twoPlace.format(test2.weibull_median(test1.Weibull_Parameters(fireintervalspersample)))); // log.debug("mean \t\t sigma \t\t mode \t\t skewness"); // log.debug(twoPlace.format(test1.weibull_mean(test2.Weibull_Parameters(fireintervalspersample)))+"\t\t"+twoPlace.format(test1.weibull_sigma(test2.Weibull_Parameters(fireintervalspersample)))+"\t\t"+twoPlace.format(test2.weibull_mode(test1.Weibull_Parameters(fireintervalspersample)))+"\t\t"+twoPlace.format(test1.weibull_skew(test2.Weibull_Parameters(fireintervalspersample)))); // log.debug("maxhazard \t\t lei \t\t uei "); // log.debug(twoPlace.format(test2.maxhazard_int(test2.Weibull_Parameters(fireintervalspersample)))+"\t\t"+twoPlace.format(test2.weibull_lowuppexcint(test2.Weibull_Parameters(fireintervalspersample))[0])+"\t\t"+twoPlace.format(test2.weibull_lowuppexcint(test2.Weibull_Parameters(fireintervalspersample))[1])); // log.debug("the size of YearWith Fires is "+YearsWithFires.size()); // log.debug("the size of the prb exdc is // "+test2.weibull_Exprob(test2.Weibull_Parameters(fireintervalspersample)).length); System.out.println( "the size of the prb exdc sample is " + weibull.getExceedenceProbability().length); for (int kk = 0; kk < weibull.getExceedenceProbability().length; kk++) { ExceeProbsample[kk][i] = weibull.getExceedenceProbability()[kk]; log.debug("file " + i + " Exce probability " + ExceeProbsample[kk][i]); // log.debug("the size is "+ExceeProbsample.length); } } // end of if at least 4 fireintervals else { enoughIntSamp[i] = false; } } // end of if jRadioSample selected. // log.debug("the size of exceeprobsample is "ExceeProbsample.length+" X "+ExceeProbsample[0].length); } // end of i readering each file loop do loop (354-1185) /* * */ // log.debug("size of the climateMatrixSite is "+climateMatrixSite.size()+" X "+climateMatrixSite.get(0).size()); // for (int j = 0; j < listYears.size(); j++){ // log.debug(climateMatrixSite.get(0).get(j) + " " + // listYears.get(j)); // } // setCursor(Cursor.getDefaultCursor()); /* * create JFileChooser object to generate a browsing capabilities */ JFileChooser fileBrowse = new JFileChooser(); fileBrowse = new JFileChooser(savePath.substring(0, savePath.lastIndexOf(File.separator))); /* * set multiselect on (even though we don't need it) */ fileBrowse.setMultiSelectionEnabled(true); /* * set file and folder directive */ fileBrowse.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES); /* * set file type: coma delimited file csv */ // FileFilter filter1 = new CSVFileFilter(); fileBrowse.setFileFilter(filter1); /* * set dialog text: select the name and location of the matrix files */ fileBrowse.setDialogTitle("Select the name and location of the Stats Summary file:"); /* * create the writer object for each of the files to be created */ Writer wr; Writer wrWDE; Writer wrSample; Writer wrWDESample; /* * set delimiter in this case we are using comas "," */ String delim = ","; /* * Start writing information into the files */ try { if (analysisType.equals(AnalysisType.COMPOSITE)) { wr = new BufferedWriter(new FileWriter(summaryFile)); wrWDE = new BufferedWriter(new FileWriter(exceedenceFile)); /* * write the heading to the files */ String buffer = ""; buffer = buffer + "Composite Parameters" + delim; for (int i = 0; i < inputFileArray.length; i++) { buffer = buffer + inputFileArray[i].getLabel() + delim; } ; wr.write(buffer.substring(0, buffer.length() - 1) + System.getProperty("line.separator")); buffer = ""; for (int j = 0; j < statsparam.length; j++) { buffer = buffer + statsparam[j] + delim; for (int k = 0; k < inputFileArray.length; k++) { if (j == 0) { if (numberOfintervalscomp[k] < 3) { buffer = buffer + twoPlace.format(numberOfintervalscomp[k]) + delim; } else { buffer = buffer + twoPlace.format(summaryComp[0][k]) + delim; } } else { if (enoughIntComp[k]) { if (summaryComp[j][k] == -99) { buffer = buffer + "" + delim; } else { buffer = buffer + twoPlace.format(summaryComp[j][k]) + delim; } } else { buffer = buffer + "" + delim; } } } // end of k loop filearray wr.write(buffer.substring(0, buffer.length() - 1) + System.getProperty("line.separator")); buffer = ""; } // end of j loop Stats // wr.close(); // // // wrWDE = new BufferedWriter(new // FileWriter(outputWDExceeTable)); /* * write the heading to the files */ buffer = ""; wrWDE.write("Exceedence Prob" + delim); for (int i = 0; i < inputFileArray.length; i++) { buffer = buffer + inputFileArray[i].getLabel() + delim; } wrWDE.write(buffer.substring(0, buffer.length() - 1) + System.getProperty("line.separator")); buffer = ""; for (int j = 0; j < fixvalt.length; j++) { buffer = buffer + threePlace.format(fixvalt[j]) + delim; for (int k = 0; k < inputFileArray.length; k++) { if (enoughIntComp[k]) { buffer = buffer + twoPlace.format(ExceeProbcomp[j][k]) + delim; } else { buffer = buffer + "" + delim; } } wrWDE.write(buffer.substring(0, buffer.length() - 1) + System.getProperty("line.separator")); buffer = ""; } wr.close(); wrWDE.close(); } // end of if jRadioComp is selecte if (analysisType.equals(AnalysisType.SAMPLE)) { wrSample = new BufferedWriter(new FileWriter(summaryFile)); wrWDESample = new BufferedWriter(new FileWriter(exceedenceFile)); /* * write the heading to the files */ wrSample.write("Sample Parameters" + delim); for (int i = 0; i < inputFileArray.length; i++) { wrSample.write(inputFileArray[i].getLabel() + delim); } wrSample.write(System.getProperty("line.separator")); for (int j = 0; j < statsparam.length; j++) { wrSample.write(statsparam[j] + delim); for (int k = 0; k < inputFileArray.length; k++) { if (j == 0) { if (numberOfintervalssamp[k] < 3) { wrSample.write(twoPlace.format(numberOfintervalssamp[k]) + delim); } else { wrSample.write(twoPlace.format(summarySample[0][k]) + delim); } } else { if (enoughIntSamp[k]) { if (summarySample[j][k] == -99) { wrSample.write("" + delim); } else { wrSample.write(twoPlace.format(summarySample[j][k]) + delim); } } else { wrSample.write("" + delim); } } } // end of k loop file array wrSample.write(System.getProperty("line.separator")); } // end of loop j loop stats // wrSample.close(); // // // log.debug("the size is "+fixvalt.length+" X "+inputFile.length); // wrWDESample = new BufferedWriter(new // FileWriter(outputWDExceeTablesample)); /* * write the heading to the files */ wrWDESample.write("Exceedence Prob" + delim); for (int i = 0; i < inputFileArray.length; i++) { wrWDESample.write(inputFileArray[i].getLabel() + delim); } wrWDESample.write(System.getProperty("line.separator")); for (int j = 0; j < fixvalt.length; j++) { wrWDESample.write(threePlace.format(fixvalt[j]) + delim); for (int k = 0; k < inputFileArray.length; k++) { // System.out.print(ExceeProbcomp[j][k]+delim); if (enoughIntSamp[k]) { wrWDESample.write(twoPlace.format(ExceeProbsample[j][k]) + delim); } else { wrWDESample.write("" + delim); } } // System.out.print(System.getProperty("line.separator")); wrWDESample.write(System.getProperty("line.separator")); } wrSample.close(); wrWDESample.close(); } // end of jradiosample } // end of Try catch (IOException ex) { ex.printStackTrace(); } finally { } }
From source file:org.fhaes.gui.ShapeFileDialog.java
/** * Prompt the user for an output filename * /* w w w.j av a2 s . c om*/ * @param filter * @return */ private File getOutputFile(FileFilter filter) { String lastVisitedFolder = App.prefs.getPref(PrefKey.PREF_LAST_EXPORT_FOLDER, null); File outputFile; // Create a file chooser final JFileChooser fc = new JFileChooser(lastVisitedFolder); fc.setAcceptAllFileFilterUsed(true); if (filter != null) { fc.addChoosableFileFilter(filter); fc.setFileFilter(filter); } fc.setFileSelectionMode(JFileChooser.FILES_ONLY); fc.setMultiSelectionEnabled(false); fc.setDialogTitle("Save as..."); // In response to a button click: int returnVal = fc.showSaveDialog(this); if (returnVal == JFileChooser.APPROVE_OPTION) { outputFile = fc.getSelectedFile(); if (FileUtils.getExtension(outputFile.getAbsolutePath()) == "") { log.debug("Output file extension not set by user"); if (fc.getFileFilter().getDescription().equals(new SHPFileFilter().getDescription())) { log.debug("Adding shp extension to output file name"); outputFile = new File(outputFile.getAbsolutePath() + ".shp"); } } else { log.debug("Output file extension set my user to '" + FileUtils.getExtension(outputFile.getAbsolutePath()) + "'"); } App.prefs.setPref(PrefKey.PREF_LAST_EXPORT_FOLDER, outputFile.getAbsolutePath()); } else { return null; } if (outputFile.exists()) { Object[] options = { "Overwrite", "No", "Cancel" }; int response = JOptionPane.showOptionDialog(this, "The file '" + outputFile.getName() + "' already exists. Are you sure you want to overwrite?", "Confirm", JOptionPane.YES_NO_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE, null, // do not use a custom Icon options, // the titles of buttons options[0]); // default button title if (response != JOptionPane.YES_OPTION) { return null; } } return outputFile; }
From source file:org.javaswift.cloudie.CloudiePanel.java
protected void onCreateStoredObject() { Container container = getSelectedContainer(); JFileChooser chooser = new JFileChooser(); chooser.setMultiSelectionEnabled(true); chooser.setCurrentDirectory(lastFolder); if (chooser.showOpenDialog(this) == JFileChooser.APPROVE_OPTION) { File[] selectedFiles = chooser.getSelectedFiles(); ops.createStoredObjects(container, selectedFiles, callback); lastFolder = chooser.getCurrentDirectory(); }/* www.jav a 2 s. c o m*/ }
From source file:org.jax.haplotype.io.SnpStreamUtil.java
/** * A main for snp data conversion/*from ww w .j a v a 2 s . c om*/ * @param args * dont care * @throws IOException * if we get one */ public static void main(String[] args) throws IOException { JFileChooser inputFileChooser = new JFileChooser(); inputFileChooser.setDialogTitle("Select CSV Chromosome Input Files"); inputFileChooser.setMultiSelectionEnabled(true); inputFileChooser.setFileSelectionMode(JFileChooser.FILES_ONLY); int userSelection = inputFileChooser.showOpenDialog(null); if (userSelection == JFileChooser.APPROVE_OPTION) { JFileChooser outputDirectoryChooser = new JFileChooser(); outputDirectoryChooser.setDialogTitle("Select an Output Directory"); outputDirectoryChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); int outputUserSelection = outputDirectoryChooser.showOpenDialog(null); if (outputUserSelection == JFileChooser.APPROVE_OPTION) { File selectedOutputDirectory = outputDirectoryChooser.getSelectedFile(); File[] selectedInputFiles = inputFileChooser.getSelectedFiles(); for (File selectedInputFile : selectedInputFiles) { writeBinaryChromosomeData(new GenotypeParser(), selectedInputFile, selectedOutputDirectory); } } } else { System.out.println("user doesn't want to open the file"); } }
From source file:org.jcurl.core.jnlp.FileDialogSwing.java
private static JFileChooser createFileChooser(final String pathHint, final String[] extensions, final boolean showDir) { final JFileChooser fc = new JFileChooser(); fc.setMultiSelectionEnabled(false); fc.setAcceptAllFileFilterUsed(true); fc.setFileFilter(new FileFilter() { @Override/*www. j a v a 2 s . c o m*/ public boolean accept(final File f) { if (f == null) return false; if (showDir && f.isDirectory()) return true; for (final String element : extensions) if (f.getName().endsWith("." + element)) return true; return false; } @Override public String getDescription() { final StringBuilder b = new StringBuilder(); for (final String element : extensions) b.append("*.").append(element).append(", "); if (b.length() > 0) b.setLength(b.length() - 2); return b.toString(); } }); return fc; }
From source file:org.jdal.system.SystemUtils.java
public static byte[] getFileAsByteArray() { JFileChooser chooser = new JFileChooser(); chooser.setMultiSelectionEnabled(false); if (JFileChooser.APPROVE_OPTION == chooser.showOpenDialog(null)) { File file = chooser.getSelectedFile(); try {/*from w w w .j a v a2 s . c o m*/ return FileUtils.readFileToByteArray(file); } catch (IOException e) { log.error(e); } } return null; }
From source file:org.jets3t.apps.cockpitlite.CockpitLite.java
/** * Event handler for this application, handles all menu items. *//*from ww w.j av a2 s. com*/ public void actionPerformed(ActionEvent event) { if (event.getSource().equals(loginButton)) { new Thread() { @Override public void run() { listObjects(); } }.start(); } // Object Events else if ("ViewObjectProperties".equals(event.getActionCommand())) { listObjectProperties(); } else if ("RefreshObjects".equals(event.getActionCommand())) { new Thread() { @Override public void run() { listObjects(); } }.start(); } else if ("TogglePublicPrivate".equals(event.getActionCommand())) { new Thread() { @Override public void run() { S3Object object = getSelectedObjects()[0]; String aclStatus = objectTableModel.getObjectAclStatus(object); boolean originalAclWasPublic = ACL_PUBLIC_DESCRIPTION.equals(aclStatus); ToggleAclDialog dialog = new ToggleAclDialog(ownerFrame, originalAclWasPublic, null, cockpitLiteProperties.getProperties()); dialog.setVisible(true); // Update ACL setting. S3Object minimalObject = new S3Object(object.getKey()); AccessControlList newAcl = (dialog.isPublicAclSet() ? AccessControlList.REST_CANNED_PUBLIC_READ : AccessControlList.REST_CANNED_PRIVATE); if (newAcl != null) { if (AccessControlList.REST_CANNED_PRIVATE.equals(newAcl)) { minimalObject.addMetadata(Constants.REST_HEADER_PREFIX + "acl", "private"); } else if (AccessControlList.REST_CANNED_PUBLIC_READ.equals(newAcl)) { minimalObject.addMetadata(Constants.REST_HEADER_PREFIX + "acl", "public-read"); } } updateObjectsAccessControlLists(new S3Object[] { minimalObject }, newAcl); dialog.dispose(); } }.start(); } else if ("GeneratePublicGetURL".equals(event.getActionCommand())) { generatePublicGetUrl(); } else if ("DeleteObjects".equals(event.getActionCommand())) { deleteSelectedObjects(); } else if ("DownloadObjects".equals(event.getActionCommand())) { try { downloadSelectedObjects(); } catch (Exception ex) { String message = "Unable to download objects from S3"; log.error(message, ex); ErrorDialog.showDialog(ownerFrame, this, cockpitLiteProperties.getProperties(), message, ex); } } else if ("UploadFiles".equals(event.getActionCommand())) { JFileChooser fileChooser = new JFileChooser(); fileChooser.setMultiSelectionEnabled(true); fileChooser.setDialogTitle("Choose file(s) to upload"); fileChooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES); fileChooser.setApproveButtonText("Upload files"); fileChooser.setCurrentDirectory(fileChoosersLastUploadDirectory); int returnVal = fileChooser.showOpenDialog(ownerFrame); if (returnVal != JFileChooser.APPROVE_OPTION) { return; } final File[] uploadFiles = fileChooser.getSelectedFiles(); if (uploadFiles.length == 0) { return; } // Save the chosen directory location for next time. fileChoosersLastUploadDirectory = uploadFiles[0].getParentFile(); new Thread() { @Override public void run() { prepareForFilesUpload(uploadFiles); } }.start(); } else if (event.getSource().equals(filterObjectsCheckBox)) { if (filterObjectsCheckBox.isSelected()) { filterObjectsPanel.setVisible(true); } else { filterObjectsPanel.setVisible(false); filterObjectsPrefix.setText(""); } } // Ooops... else { log.warn("Unrecognised ActionEvent command '" + event.getActionCommand() + "' in " + event); } }
From source file:org.jets3t.apps.cockpitlite.CockpitLite.java
/** * Prepares to perform a download of objects from S3 by prompting the user for a directory * to store the files in, then performing the download. * * @throws IOException/*from w w w .j a v a2s . c o m*/ */ private void downloadSelectedObjects() throws IOException { // Prompt user to choose directory location for downloaded files (or cancel download altogether) JFileChooser fileChooser = new JFileChooser(); fileChooser.setDialogTitle("Choose directory to save S3 files in"); fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); fileChooser.setMultiSelectionEnabled(false); fileChooser.setSelectedFile(downloadDirectory); int returnVal = fileChooser.showDialog(ownerFrame, "Choose Directory"); if (returnVal != JFileChooser.APPROVE_OPTION) { return; } downloadDirectory = fileChooser.getSelectedFile(); prepareForObjectsDownload(); }
From source file:org.kse.gui.actions.ImportCaReplyFromFileAction.java
private File chooseCaFile() { JFileChooser chooser = FileChooserFactory.getCaReplyFileChooser(); chooser.setCurrentDirectory(CurrentDirectory.get()); chooser.setDialogTitle(res.getString("ImportCaReplyFromFileAction.ImportCaReply.Title")); chooser.setMultiSelectionEnabled(false); int rtnValue = chooser.showDialog(frame, res.getString("ImportCaReplyFromFileAction.ImportCaReply.button")); if (rtnValue == JFileChooser.APPROVE_OPTION) { File openFile = chooser.getSelectedFile(); CurrentDirectory.updateForFile(openFile); return openFile; }//from w w w . ja v a 2 s.c o m return null; }