X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=9818e6b08c500b2dd9601ddea816fdd354e7fe89;hb=80916c21f32a24ec777b51c758df0cc2f57f6bb8;hp=198c3bd66739f9b67afe2e6383d5e87cb8cb7c83;hpb=1c66dc9053356a709e9cd9d3282517b5221f1ba2;p=jalview.git diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 198c3bd..9818e6b 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -1,18 +1,18 @@ /* * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle - * + * * This file is part of Jalview. - * + * * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License + * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. - * + * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -127,7 +127,7 @@ import javax.swing.SwingUtilities; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @@ -146,7 +146,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, AlignViewport viewport; Vector alignPanels = new Vector(); - + /** * Last format used to load or save alignments in this window */ @@ -159,7 +159,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a new AlignFrame object with specific width and height. - * + * * @param al * @param width * @param height @@ -172,7 +172,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId - * + * * @param al * @param width * @param height @@ -187,7 +187,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Creates a new AlignFrame object with specific width, height and * sequenceSetId - * + * * @param al * @param width * @param height @@ -202,7 +202,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * new alignment window with hidden columns - * + * * @param al * AlignmentI * @param hiddenColumns @@ -221,7 +221,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId - * + * * @param al * @param hiddenColumns * @param width @@ -238,7 +238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Create alignment frame for al with hiddenColumns, a specific width and * height, and specific sequenceId - * + * * @param al * @param hiddenColumns * @param width @@ -267,7 +267,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Make a new AlignFrame from exisiting alignmentPanels - * + * * @param ap * AlignmentPanel * @param av @@ -335,7 +335,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Change the filename and format for the alignment, and enable the 'reload' * button functionality. - * + * * @param file * valid filename * @param format @@ -352,6 +352,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { addKeyListener(new KeyAdapter() { + @Override public void keyPressed(KeyEvent evt) { if (viewport.cursorMode @@ -532,6 +533,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void keyReleased(KeyEvent evt) { switch (evt.getKeyCode()) @@ -616,6 +618,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Desktop.instance.addJalviewPropertyChangeListener("services", thisListener = new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { // // System.out.println("Discoverer property change."); @@ -624,6 +627,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { System.err @@ -637,6 +641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -649,6 +654,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // Finally, build the menu once to get current service state new Thread(new Runnable() { + @Override public void run() { BuildWebServiceMenu(); @@ -685,7 +691,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Need to call this method when tabs are selected for multiple views, or when * loading from Jalview2XML.java - * + * * @param av * AlignViewport */ @@ -718,7 +724,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showSeqFeatures.setSelected(av.showSequenceFeatures); hiddenMarkers.setState(av.showHiddenMarkers); - applyToAllGroups.setState(av.colourAppliesToAllGroups); + applyToAllGroups.setState(av.getColourAppliesToAllGroups()); showNpFeatsMenuitem.setSelected(av.isShowNpFeats()); showDbRefsMenuitem.setSelected(av.isShowDbRefs()); autoCalculate.setSelected(av.autoCalculateConsensus); @@ -731,14 +737,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, updateEditMenuBar(); } - + // methods for implementing IProgressIndicator + // need to refactor to a reusable stub class Hashtable progressBars, progressBarHandlers; /* * (non-Javadoc) - * + * * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long) */ + @Override public void setProgressBar(String message, long id) { if (progressBars == null) @@ -786,6 +794,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, validate(); } + @Override public void registerHandler(final long id, final IProgressIndicatorHandler handler) { @@ -803,6 +812,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, cancel.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); @@ -817,9 +827,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @return true if any progress bars are still active */ + @Override public boolean operationInProgress() { if (progressBars != null && progressBars.size() > 0) @@ -842,20 +853,25 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); } + @Override public void fetchSequence_actionPerformed(ActionEvent e) { new SequenceFetcher(this); } + @Override public void addFromFile_actionPerformed(ActionEvent e) { Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport); } + @Override public void reload_actionPerformed(ActionEvent e) { if (fileName != null) { + // TODO: JAL-1108 - ensure all associated frames are closed regardless of + // originating file's format // TODO: work out how to recover feature settings for correct view(s) when // file is reloaded. if (currentFileFormat.equals("Jalview")) @@ -864,7 +880,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, for (int i = 0; i < frames.length; i++) { if (frames[i] instanceof AlignFrame && frames[i] != this - && ((AlignFrame) frames[i]).fileName.equals(fileName)) + && ((AlignFrame) frames[i]).fileName!=null && ((AlignFrame) frames[i]).fileName.equals(fileName)) { try { @@ -901,6 +917,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final FeatureSettings nfs = newframe.featureSettings; SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { nfs.frame.setBounds(fspos); @@ -914,16 +931,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void addFromText_actionPerformed(ActionEvent e) { Desktop.instance.inputTextboxMenuItem_actionPerformed(viewport); } + @Override public void addFromURL_actionPerformed(ActionEvent e) { Desktop.instance.inputURLMenuItem_actionPerformed(viewport); } + @Override public void save_actionPerformed(ActionEvent e) { if (fileName == null @@ -941,10 +961,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void saveAs_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -1038,7 +1059,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, FormatAdapter f = new FormatAdapter(); String output = f.formatSequences( format, - (Alignment) viewport.getAlignment(), // class cast exceptions will + viewport.getAlignment(), // class cast exceptions will // occur in the distant future omitHidden, f.getCacheSuffixDefault(format), viewport.getColumnSelection()); @@ -1093,10 +1114,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void outputText_actionPerformed(ActionEvent e) { String[] omitHidden = null; @@ -1138,10 +1160,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void htmlMenuItem_actionPerformed(ActionEvent e) { new HTMLOutput(alignPanel, @@ -1156,10 +1179,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void createPNG(File f) { alignPanel.makePNG(f); @@ -1167,15 +1191,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void createEPS(File f) { alignPanel.makeEPS(f); } + @Override public void pageSetup_actionPerformed(ActionEvent e) { PrinterJob printJob = PrinterJob.getPrinterJob(); @@ -1184,10 +1210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void printMenuItem_actionPerformed(ActionEvent e) { // Putting in a thread avoids Swing painting problems @@ -1195,11 +1222,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, thread.start(); } + @Override public void exportFeatures_actionPerformed(ActionEvent e) { new AnnotationExporter().exportFeatures(alignPanel); } + @Override public void exportAnnotations_actionPerformed(ActionEvent e) { new AnnotationExporter().exportAnnotations(alignPanel, @@ -1209,6 +1238,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, .getAlignment()).alignmentProperties); } + @Override public void associatedData_actionPerformed(ActionEvent e) { // Pick the tree file @@ -1232,9 +1262,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Close the current view or all views in the alignment frame. If the frame * only contains one view then the alignment will be removed from memory. - * + * * @param closeAllTabs */ + @Override public void closeMenuItem_actionPerformed(boolean closeAllTabs) { if (alignPanels != null && alignPanels.size() < 2) @@ -1277,7 +1308,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * close alignPanel2 and shuffle tabs appropriately. - * + * * @param alignPanel2 */ public void closeView(AlignmentPanel alignPanel2) @@ -1353,7 +1384,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @return alignment objects for all views */ AlignmentI[] getViewAlignments() @@ -1378,10 +1409,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void undoMenuItem_actionPerformed(ActionEvent e) { if (viewport.historyList.empty()) @@ -1413,10 +1445,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void redoMenuItem_actionPerformed(ActionEvent e) { if (viewport.redoList.size() < 1) @@ -1494,7 +1527,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param up * DOCUMENT ME! */ @@ -1506,61 +1539,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { return; } - - if (up) - { - for (int i = 1; i < viewport.getAlignment().getHeight(); i++) - { - SequenceI seq = viewport.getAlignment().getSequenceAt(i); - - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1); - - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.getAlignment().getSequences().setElementAt(temp, i); - viewport.getAlignment().getSequences().setElementAt(seq, i - 1); - } - } - else - { - for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--) - { - SequenceI seq = viewport.getAlignment().getSequenceAt(i); - - if (!sg.getSequences(null).contains(seq)) - { - continue; - } - - SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1); - - if (sg.getSequences(null).contains(temp)) - { - continue; - } - - viewport.getAlignment().getSequences().setElementAt(temp, i); - viewport.getAlignment().getSequences().setElementAt(seq, i + 1); - } - } - + viewport.getAlignment().moveSelectedSequencesByOne(sg, viewport.getHiddenRepSequences(), up); alignPanel.paintAlignment(true); } synchronized void slideSequences(boolean right, int size) { - Vector sg = new Vector(); + List sg = new Vector(); if (viewport.cursorMode) { - sg.addElement(viewport.getAlignment().getSequenceAt( + sg.add(viewport.getAlignment().getSequenceAt( alignPanel.seqPanel.seqCanvas.cursorY)); } else if (viewport.getSelectionGroup() != null @@ -1584,9 +1572,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, invertGroup.add(viewport.getAlignment().getSequenceAt(i)); } - SequenceI[] seqs1 = new SequenceI[sg.size()]; - for (int i = 0; i < sg.size(); i++) - seqs1[i] = (SequenceI) sg.elementAt(i); + SequenceI[] seqs1 = sg.toArray(new SequenceI[0]); SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; for (int i = 0; i < invertGroup.size(); i++) @@ -1641,10 +1627,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void copy_actionPerformed(ActionEvent e) { System.gc(); @@ -1709,10 +1696,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void pasteNew_actionPerformed(ActionEvent e) { paste(true); @@ -1720,10 +1708,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void pasteThis_actionPerformed(ActionEvent e) { paste(false); @@ -1731,7 +1720,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Paste contents of Jalview clipboard - * + * * @param newAlignment * true to paste to a new alignment, otherwise add to this. */ @@ -1792,6 +1781,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } int alwidth = 0; + ArrayList newGraphGroups=new ArrayList(); + int fgroup=-1; if (newAlignment) { @@ -1859,6 +1850,16 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { newDs.clear(); // tidy up } + if (alignment.getAlignmentAnnotation()!=null) + { + for (AlignmentAnnotation alan:alignment.getAlignmentAnnotation()) + { + if (alan.graphGroup>fgroup) + { + fgroup=alan.graphGroup; + } + } + } if (pastedal.getAlignmentAnnotation() != null) { // Add any annotation attached to alignment. @@ -1869,6 +1870,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (alann[i].sequenceRef == null && !alann[i].autoCalculated) { AlignmentAnnotation newann = new AlignmentAnnotation(alann[i]); + if (newann.graphGroup>-1) + { + if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null) + { + for (int q=newGraphGroups.size();q<=newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup,new Integer(++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue(); + } + newann.padAnnotation(alwidth); alignment.addAnnotation(newann); } @@ -1888,11 +1902,28 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (sequences[i].getAnnotation() != null) { + AlignmentAnnotation newann; for (int a = 0; a < sequences[i].getAnnotation().length; a++) { annotationAdded = true; - sequences[i].getAnnotation()[a].adjustForAlignment(); - sequences[i].getAnnotation()[a].padAnnotation(alwidth); + newann=sequences[i].getAnnotation()[a]; + newann.adjustForAlignment(); + newann.padAnnotation(alwidth); + if (newann.graphGroup>-1) + { + if (newann.graphGroup>-1) + { + if (newGraphGroups.size()<=newann.graphGroup || newGraphGroups.get(newann.graphGroup)==null) + { + for (int q=newGraphGroups.size();q<=newann.graphGroup; q++) + { + newGraphGroups.add(q, null); + } + newGraphGroups.set(newann.graphGroup,new Integer(++fgroup)); + } + newann.graphGroup = newGraphGroups.get(newann.graphGroup).intValue(); + } + } alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation // was // duplicated @@ -1932,6 +1963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, newann.padAnnotation(avwidth); alview[avnum].addAnnotation(newann); // annotation was // duplicated earlier + // TODO JAL-1145 graphGroups are not updated for sequence annotation added to several views. This may cause strangeness alview[avnum].setAnnotationIndex(newann, a); } } @@ -1941,6 +1973,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } viewport.firePropertyChange("alignment", null, alignment.getSequences()); + if (alignPanels!=null ) {for (AlignmentPanel ap:((Vector)alignPanels)) + { + ap.validateAnnotationDimensions(false); + }} else { alignPanel.validateAnnotationDimensions(false);} } else @@ -2000,10 +2036,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void cut_actionPerformed(ActionEvent e) { copy_actionPerformed(null); @@ -2012,10 +2049,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void delete_actionPerformed(ActionEvent evt) { @@ -2072,10 +2110,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void deleteGroups_actionPerformed(ActionEvent e) { viewport.getAlignment().deleteAllGroups(); @@ -2088,10 +2127,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = new SequenceGroup(); @@ -2110,10 +2150,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { if (viewport.cursorMode) @@ -2133,10 +2174,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2158,6 +2200,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.sendSelection(); } + @Override public void invertColSel_actionPerformed(ActionEvent e) { viewport.invertColumnSelection(); @@ -2167,10 +2210,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { trimAlignment(true); @@ -2178,10 +2222,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void remove2RightMenuItem_actionPerformed(ActionEvent e) { trimAlignment(false); @@ -2235,12 +2280,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(trimRegion); - Vector groups = viewport.getAlignment().getGroups(); - - for (int i = 0; i < groups.size(); i++) + for (SequenceGroup sg :viewport.getAlignment().getGroups()) { - SequenceGroup sg = (SequenceGroup) groups.get(i); - if ((trimLeft && !sg.adjustForRemoveLeft(column)) || (!trimLeft && !sg.adjustForRemoveRight(column))) { @@ -2255,10 +2296,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.getAlignment().getWidth() - 1; @@ -2302,10 +2344,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { int start = 0, end = viewport.getAlignment().getWidth() - 1; @@ -2340,10 +2383,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void padGapsMenuitem_actionPerformed(ActionEvent e) { viewport.setPadGaps(padGapsMenuitem.isSelected()); @@ -2363,22 +2407,24 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void findMenuItem_actionPerformed(ActionEvent e) { new Finder(); } + @Override public void newView_actionPerformed(ActionEvent e) { newView(true); } /** - * + * * @param copyAnnotation * if true then duplicate all annnotation, groups and settings * @return new alignment panel, already displayed. @@ -2389,7 +2435,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @param viewTitle * title of newly created view * @return new alignment panel, already displayed. @@ -2400,7 +2446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * + * * @param viewTitle * title of newly created view * @param copyAnnotation @@ -2482,11 +2528,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return newap; } + @Override public void expandViews_actionPerformed(ActionEvent e) { Desktop.instance.explodeViews(this); } + @Override public void gatherViews_actionPerformed(ActionEvent e) { Desktop.instance.gatherViews(this); @@ -2494,10 +2542,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { new FontChooser(alignPanel); @@ -2505,10 +2554,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void seqLimit_actionPerformed(ActionEvent e) { viewport.setShowJVSuffix(seqLimits.isSelected()); @@ -2518,12 +2568,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } + @Override public void idRightAlign_actionPerformed(ActionEvent e) { viewport.rightAlignIds = idRightAlign.isSelected(); alignPanel.paintAlignment(true); } + @Override public void centreColumnLabels_actionPerformed(ActionEvent e) { viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); @@ -2532,9 +2584,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ + @Override protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) @@ -2546,10 +2599,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void colourTextMenuItem_actionPerformed(ActionEvent e) { viewport.setColourText(colourTextMenuItem.isSelected()); @@ -2558,10 +2612,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void wrapMenuItem_actionPerformed(ActionEvent e) { scaleAbove.setVisible(wrapMenuItem.isSelected()); @@ -2571,17 +2626,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setWrapAlignment(wrapMenuItem.isSelected()); } + @Override public void showAllSeqs_actionPerformed(ActionEvent e) { viewport.showAllHiddenSeqs(); } + @Override public void showAllColumns_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); repaint(); } + @Override public void hideSelSequences_actionPerformed(ActionEvent e) { viewport.hideAllSelectedSeqs(); @@ -2590,7 +2648,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * called by key handler and the hide all/show all menu items - * + * * @param toggleSeqs * @param toggleCols */ @@ -2660,11 +2718,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt. * event.ActionEvent) */ + @Override public void hideAllButSelection_actionPerformed(ActionEvent e) { toggleHiddenRegions(false, false); @@ -2672,11 +2731,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event * .ActionEvent) */ + @Override public void hideAllSelection_actionPerformed(ActionEvent e) { SequenceGroup sg = viewport.getSelectionGroup(); @@ -2688,11 +2748,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event. * ActionEvent) */ + @Override public void showAllhidden_actionPerformed(ActionEvent e) { viewport.showAllHiddenColumns(); @@ -2700,12 +2761,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.paintAlignment(true); } + @Override public void hideSelColumns_actionPerformed(ActionEvent e) { viewport.hideSelectedColumns(); alignPanel.paintAlignment(true); } + @Override public void hiddenMarkers_actionPerformed(ActionEvent e) { viewport.setShowHiddenMarkers(hiddenMarkers.isSelected()); @@ -2714,10 +2777,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleAbove_actionPerformed(ActionEvent e) { viewport.setScaleAboveWrapped(scaleAbove.isSelected()); @@ -2726,10 +2790,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleLeft_actionPerformed(ActionEvent e) { viewport.setScaleLeftWrapped(scaleLeft.isSelected()); @@ -2738,10 +2803,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void scaleRight_actionPerformed(ActionEvent e) { viewport.setScaleRightWrapped(scaleRight.isSelected()); @@ -2750,10 +2816,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { viewport.setShowBoxes(viewBoxesMenuItem.isSelected()); @@ -2762,10 +2829,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void viewTextMenuItem_actionPerformed(ActionEvent e) { viewport.setShowText(viewTextMenuItem.isSelected()); @@ -2774,10 +2842,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { viewport.setRenderGaps(renderGapsMenuItem.isSelected()); @@ -2786,6 +2855,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public FeatureSettings featureSettings; + @Override public void featureSettings_actionPerformed(ActionEvent e) { if (featureSettings != null) @@ -2804,10 +2874,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set or clear 'Show Sequence Features' - * + * * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeatures_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeatures(showSeqFeatures.isSelected()); @@ -2820,10 +2891,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Set or clear 'Show Sequence Features' - * + * * @param evt * DOCUMENT ME! */ + @Override public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight @@ -2843,16 +2915,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { viewport.setShowAnnotation(annotationPanelMenuItem.isSelected()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected()); } + @Override public void alignmentProperties() { JEditorPane editPane = new JEditorPane("text/html", ""); @@ -2869,10 +2943,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { if (alignPanel.overviewPanel != null) @@ -2889,6 +2964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, frame.setLayer(JLayeredPane.PALETTE_LAYER); frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() { + @Override public void internalFrameClosed( javax.swing.event.InternalFrameEvent evt) { @@ -2899,6 +2975,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(overview); } + @Override public void textColour_actionPerformed(ActionEvent e) { new TextColourChooser().chooseColour(alignPanel, null); @@ -2906,10 +2983,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void noColourmenuItem_actionPerformed(ActionEvent e) { changeColour(null); @@ -2917,22 +2995,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void clustalColour_actionPerformed(ActionEvent e) { - changeColour(new ClustalxColourScheme(viewport.getAlignment() - .getSequences(), viewport.getAlignment().getWidth())); + changeColour(new ClustalxColourScheme(viewport.getAlignment(), viewport.getHiddenRepSequences())); } /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void zappoColour_actionPerformed(ActionEvent e) { changeColour(new ZappoColourScheme()); @@ -2940,10 +3019,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void taylorColour_actionPerformed(ActionEvent e) { changeColour(new TaylorColourScheme()); @@ -2951,10 +3031,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void hydrophobicityColour_actionPerformed(ActionEvent e) { changeColour(new HydrophobicColourScheme()); @@ -2962,10 +3043,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void helixColour_actionPerformed(ActionEvent e) { changeColour(new HelixColourScheme()); @@ -2973,10 +3055,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void strandColour_actionPerformed(ActionEvent e) { changeColour(new StrandColourScheme()); @@ -2984,10 +3067,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void turnColour_actionPerformed(ActionEvent e) { changeColour(new TurnColourScheme()); @@ -2995,10 +3079,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void buriedColour_actionPerformed(ActionEvent e) { changeColour(new BuriedColourScheme()); @@ -3006,15 +3091,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void nucleotideColour_actionPerformed(ActionEvent e) { changeColour(new NucleotideColourScheme()); } + @Override public void purinePyrimidineColour_actionPerformed(ActionEvent e) { changeColour(new PurinePyrimidineColourScheme()); @@ -3026,11 +3113,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation * ()[0])); } */ + @Override public void annotationColour_actionPerformed(ActionEvent e) { new AnnotationColourChooser(viewport, alignPanel); } + @Override public void rnahelicesColour_actionPerformed(ActionEvent e) { new RNAHelicesColourChooser(viewport, alignPanel); @@ -3038,10 +3127,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void applyToAllGroups_actionPerformed(ActionEvent e) { viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected()); @@ -3049,7 +3139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param cs * DOCUMENT ME! */ @@ -3102,12 +3192,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (viewport.getColourAppliesToAllGroups()) { - Vector groups = viewport.getAlignment().getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); + for (SequenceGroup sg:viewport.getAlignment().getGroups()) + { if (cs == null) { sg.cs = null; @@ -3116,8 +3204,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.getSequences(viewport - .getHiddenRepSequences()), sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg, viewport + .getHiddenRepSequences()); } else if (cs instanceof UserColourScheme) { @@ -3175,10 +3263,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void modifyPID_actionPerformed(ActionEvent e) { if (viewport.getAbovePIDThreshold() @@ -3192,10 +3281,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void modifyConservation_actionPerformed(ActionEvent e) { if (viewport.getConservationSelected() @@ -3209,10 +3299,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void conservationMenuItem_actionPerformed(ActionEvent e) { viewport.setConservationSelected(conservationMenuItem.isSelected()); @@ -3227,10 +3318,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void abovePIDThreshold_actionPerformed(ActionEvent e) { viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected()); @@ -3245,10 +3337,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void userDefinedColour_actionPerformed(ActionEvent e) { if (e.getActionCommand().equals("User Defined...")) @@ -3290,6 +3383,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, radioItem.setName("USER_DEFINED"); radioItem.addMouseListener(new MouseAdapter() { + @Override public void mousePressed(MouseEvent evt) { if (evt.isControlDown() @@ -3312,6 +3406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3323,6 +3418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, }); radioItem.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { userDefinedColour_actionPerformed(evt); @@ -3337,10 +3433,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void PIDColour_actionPerformed(ActionEvent e) { changeColour(new PIDColourScheme()); @@ -3348,10 +3445,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void BLOSUM62Colour_actionPerformed(ActionEvent e) { changeColour(new Blosum62ColourScheme()); @@ -3359,10 +3457,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3375,10 +3474,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortIDMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3390,10 +3490,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3405,10 +3506,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void sortGroupMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3421,10 +3523,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { new RedundancyPanel(alignPanel, this); @@ -3432,10 +3535,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { if ((viewport.getSelectionGroup() == null) @@ -3455,10 +3559,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void PCAMenuItem_actionPerformed(ActionEvent e) { if (((viewport.getSelectionGroup() != null) @@ -3478,6 +3583,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, new PCAPanel(alignPanel); } + @Override public void autoCalculate_actionPerformed(ActionEvent e) { viewport.autoCalculateConsensus = autoCalculate.isSelected(); @@ -3488,6 +3594,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void sortByTreeOption_actionPerformed(ActionEvent e) { viewport.sortByTree = sortByTree.isSelected(); @@ -3501,10 +3608,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "PID", "Average distance tree using PID"); @@ -3512,10 +3620,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); @@ -3523,10 +3632,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); @@ -3534,10 +3644,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); @@ -3545,7 +3656,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param type * DOCUMENT ME! * @param pwType @@ -3569,13 +3680,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return; } - int s = 0; SequenceGroup sg = viewport.getSelectionGroup(); /* Decide if the selection is a column region */ - while (s < sg.getSize()) + for (SequenceI _s:sg.getSequences()) { - if (((SequenceI) sg.getSequences(null).elementAt(s++)).getLength() < sg + if (_s.getLength() < sg .getEndRes()) { JOptionPane @@ -3633,7 +3743,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param title * DOCUMENT ME! * @param order @@ -3646,6 +3756,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3664,7 +3775,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Add a new sort by annotation score menu item - * + * * @param sort * the menu to add the option to * @param scoreLabel @@ -3678,6 +3789,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, sort.add(item); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); @@ -3700,8 +3812,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * search the alignment and rebuild the sort by annotation score submenu the * last alignment annotation vector hash is stored to minimize cost of * rebuilding in subsequence calls. - * + * */ + @Override public void buildSortByAnnotationScoresMenu() { if (viewport.getAlignment().getAlignmentAnnotation() == null) @@ -3715,10 +3828,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, // almost certainly a quicker way to do this - but we keep it simple Hashtable scoreSorts = new Hashtable(); AlignmentAnnotation aann[]; - Enumeration sq = viewport.getAlignment().getSequences().elements(); - while (sq.hasMoreElements()) + for (SequenceI sqa:viewport.getAlignment().getSequences()) { - aann = ((SequenceI) sq.nextElement()).getAnnotation(); + aann = sqa.getAnnotation(); for (int i = 0; aann != null && i < aann.length; i++) { if (aann[i].hasScore() && aann[i].sequenceRef != null) @@ -3747,12 +3859,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * call. Listeners are added to remove the menu item when the treePanel is * closed, and adjust the tree leaf to sequence mapping when the alignment is * modified. - * + * * @param treePanel * Displayed tree window. * @param title * SortBy menu item title. */ + @Override public void buildTreeMenu() { sortByTreeMenu.removeAll(); @@ -3786,6 +3899,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final NJTree tree = ((TreePanel) treePanels.elementAt(i)).getTree(); item.addActionListener(new java.awt.event.ActionListener() { + @Override public void actionPerformed(ActionEvent e) { tp.sortByTree_actionPerformed(null); @@ -3814,7 +3928,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Work out whether the whole set of sequences or just the selected set will * be submitted for multiple alignment. - * + * */ public jalview.datamodel.AlignmentView gatherSequencesForAlignment() { @@ -3829,7 +3943,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new * SequenceI[sz = seqs.getSize(false)]; - * + * * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI) * seqs.getSequenceAt(i); } */ @@ -3839,9 +3953,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { /* * Vector seqs = viewport.getAlignment().getSequences(); - * + * * if (seqs.size() > 1) { msa = new SequenceI[seqs.size()]; - * + * * for (int i = 0; i < seqs.size(); i++) { msa[i] = (SequenceI) * seqs.elementAt(i); } } */ @@ -3887,10 +4001,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * DOCUMENT ME! - * + * * @param e * DOCUMENT ME! */ + @Override protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { // Pick the tree file @@ -3925,84 +4040,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } } - - @Override - public void loadScores_actionPerformed(ActionEvent e) - { - // Pick the tree file - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Select a T-Coffee scores ascii file"); - chooser.setToolTipText("Load a score file"); - - int value = chooser.showOpenDialog(null); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String sFilePath = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", sFilePath); - - - try - { - TCoffeeScoreFile result = new TCoffeeScoreFile(sFilePath, FormatAdapter.FILE); - if (!result.isValid()) { - JOptionPane.showMessageDialog(Desktop.desktop, result.getWarningMessage(), - "Problem reading T-COFFEE score file", JOptionPane.WARNING_MESSAGE); - return; - } - - /* - * check that the score matrix matches the alignment dimensions - */ - AlignmentI aln; - if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != result.getHeight() || aln.getWidth() != result.getWidth()) ) { - // TODO: raise a dialog box here rather than bomb out. - throw new RuntimeException("The scores matrix does not match the alignment dimensions"); - } - if (result.annotateAlignment(alignPanel.getAlignment(), true)) - { - tcoffeeColour.setEnabled(true); - tcoffeeColour.setSelected(true); - // switch to this color - changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); - } else { - tcoffeeColour.setEnabled(false); - tcoffeeColour.setSelected(false); - } - } - catch (Exception ex) { - JOptionPane.showMessageDialog( - Desktop.desktop, - ex.getMessage(), - "Problem reading tree file", - JOptionPane.WARNING_MESSAGE); - - ex.printStackTrace(); - } - } - - } - - - @Override - protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) { - changeColour( new TCoffeeColourScheme(alignPanel.getAlignment()) ); - } - -// /** -// * Load the (T-Coffee) score file from the specified url -// * -// * @param url The absolute path from where download and read the score file -// * @throws IOException -// */ -// public void loadScoreFile(URL url ) throws IOException { -// -// TCoffeeScoreFile result = new TCoffeeScoreFile(); -// result.parse( new InputStreamReader( url.openStream() ) ); -// tcoffeeScoreFile = result; -// } - + + @Override + protected void tcoffeeColorScheme_actionPerformed(ActionEvent e) + { + changeColour(new TCoffeeColourScheme(alignPanel.getAlignment())); + } + public TreePanel ShowNewickTree(NewickFile nf, String title) { return ShowNewickTree(nf, title, 600, 500, 4, 5); @@ -4023,7 +4067,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Add a treeviewer for the tree extracted from a newick file object to the * current alignment view - * + * * @param nf * the tree * @param title @@ -4074,7 +4118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Generates menu items and listener event actions for web service clients - * + * */ public void BuildWebServiceMenu() { @@ -4093,6 +4137,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, buildingMenu = true; new Thread(new Runnable() { + @Override public void run() { try @@ -4116,7 +4161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, "Secondary Structure Prediction"); final JMenu seqsrchmenu = new JMenu("Sequence Database Search"); final JMenu analymenu = new JMenu("Analysis"); - final JMenu dismenu = new JMenu("Disorder"); + final JMenu dismenu = new JMenu("Protein Disorder"); // JAL-940 - only show secondary structure prediction services from // the legacy server if (// Cache.getDefault("SHOW_JWS1_SERVICES", true) @@ -4191,6 +4236,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { try @@ -4201,7 +4247,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { for (int i = 0, j = wsmenu.size(); i < j; i++) { - webService.add((JMenu) wsmenu.get(i)); + webService.add(wsmenu.get(i)); } } else @@ -4243,6 +4289,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } catch (Exception e) { + Cache.log.debug("Exception during web service menu building process.",e); } ; } @@ -4260,7 +4307,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * construct any groupURL type service menu entries. - * + * * @param webService */ private void build_urlServiceMenu(JMenu webService) @@ -4270,12 +4317,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final * AlignFrame af = this; testAlView.addActionListener(new ActionListener() { - * + * * @Override public void actionPerformed(ActionEvent e) { * jalview.datamodel.AlignmentView * .testSelectionViews(af.viewport.getAlignment(), * af.viewport.getColumnSelection(), af.viewport.selectionGroup); } - * + * * }); webService.add(testAlView); */ // TODO: refactor to RestClient discoverer and merge menu entries for @@ -4302,12 +4349,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * public void vamsasStore_actionPerformed(ActionEvent e) { JalviewFileChooser * chooser = new JalviewFileChooser(jalview.bin.Cache. * getProperty("LAST_DIRECTORY")); - * + * * chooser.setFileView(new JalviewFileView()); chooser.setDialogTitle("Export * to Vamsas file"); chooser.setToolTipText("Export"); - * + * * int value = chooser.showSaveDialog(this); - * + * * if (value == JalviewFileChooser.APPROVE_OPTION) { * jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport); * //vs.store(chooser.getSelectedFile().getAbsolutePath() ); vs.storeJalview( @@ -4315,7 +4362,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, */ /** * prototype of an automatically enabled/disabled analysis function - * + * */ protected void setShowProductsEnabled() { @@ -4335,7 +4382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * search selection for sequence xRef products and build the show products * menu. - * + * * @param selection * @param dataset * @return true if showProducts menu should be enabled. @@ -4365,6 +4412,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, xtype.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: new thread for this call with vis-delay @@ -4398,6 +4446,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Runnable foo = new Runnable() { + @Override public void run() { final long sttime = System.currentTimeMillis(); @@ -4481,6 +4530,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void showProducts_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4514,6 +4564,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void showTranslation_actionPerformed(ActionEvent e) { // ///////////////////////////// @@ -4552,7 +4603,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Try to load a features file onto the alignment. - * + * * @param file * contents or path to retrieve file * @param type @@ -4592,22 +4643,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return featuresFile; } + @Override public void dragEnter(DropTargetDragEvent evt) { } + @Override public void dragExit(DropTargetEvent evt) { } + @Override public void dragOver(DropTargetDragEvent evt) { } + @Override public void dropActionChanged(DropTargetDragEvent evt) { } + @Override public void drop(DropTargetDropEvent evt) { Transferable t = evt.getTransferable(); @@ -4796,7 +4852,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * it's and Annotation file, then a JNet file, and finally a features file. If * all are false then the user may have dropped an alignment file onto this * AlignFrame. - * + * * @param file * either a filename or a URL string. */ @@ -4819,54 +4875,92 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (!isAnnotation) { - // try to see if its a JNet 'concise' style annotation file *before* we - // try to parse it as a features file - if (format == null) + // first see if its a T-COFFEE score file + TCoffeeScoreFile tcf = null; + try { - format = new IdentifyFile().Identify(file, protocol); - } - if (format.equalsIgnoreCase("JnetFile")) + tcf = new TCoffeeScoreFile(file, protocol); + if (tcf.isValid()) + { + if (tcf.annotateAlignment(viewport.getAlignment(), true)) + { + tcoffeeColour.setEnabled(true); + tcoffeeColour.setSelected(true); + changeColour(new TCoffeeColourScheme(viewport.getAlignment())); + isAnnotation = true; + statusBar + .setText("Successfully pasted T-Coffee scores to alignment."); + } + else + { + // some problem - if no warning its probable that the ID matching process didn't work + JOptionPane.showMessageDialog(Desktop.desktop, + tcf.getWarningMessage()==null ? "Check that the file matches sequence IDs in the alignment." : tcf.getWarningMessage(), + "Problem reading T-COFFEE score file", + JOptionPane.WARNING_MESSAGE); + } + } + else + { + tcf = null; + } + } catch (Exception x) { - jalview.io.JPredFile predictions = new jalview.io.JPredFile(file, - protocol); - new JnetAnnotationMaker().add_annotation(predictions, - viewport.getAlignment(), 0, false); - isAnnotation = true; + Cache.log.debug("Exception when processing data source as T-COFFEE score file",x); + tcf = null; } - else + if (tcf == null) { - /* - * if (format.equalsIgnoreCase("PDB")) { - * - * String pdbfn = ""; // try to match up filename with sequence id try - * { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = new - * File(file); pdbfn = fl.getName(); } else if (protocol == - * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = - * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == null) - * { SequenceIdMatcher idm = new SequenceIdMatcher(viewport - * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { // - * attempt to find a match in the alignment SequenceI mtch = - * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while - * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > l) - * { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch = - * idm.findIdMatch(pdbfn); } if (mtch != null) { // try and associate - * // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() - * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) { - * System.err.println("Associated file : " + file + " with " + - * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // - * TODO: maybe need to load as normal otherwise return; } } - */ + // try to see if its a JNet 'concise' style annotation file *before* + // we // try to parse it as a features file - boolean isGroupsFile = parseFeaturesFile(file, protocol); - // if it wasn't a features file then we just treat it as a general - // alignment file to load into the current view. - if (!isGroupsFile) + if (format == null) + { + format = new IdentifyFile().Identify(file, protocol); + } + if (format.equalsIgnoreCase("JnetFile")) { - new FileLoader().LoadFile(viewport, file, protocol, format); + jalview.io.JPredFile predictions = new jalview.io.JPredFile( + file, protocol); + new JnetAnnotationMaker().add_annotation(predictions, + viewport.getAlignment(), 0, false); + isAnnotation = true; } else { - alignPanel.paintAlignment(true); + /* + * if (format.equalsIgnoreCase("PDB")) { + * + * String pdbfn = ""; // try to match up filename with sequence id + * try { if (protocol == jalview.io.FormatAdapter.FILE) { File fl = + * new File(file); pdbfn = fl.getName(); } else if (protocol == + * jalview.io.FormatAdapter.URL) { URL url = new URL(file); pdbfn = + * url.getFile(); } } catch (Exception e) { } ; if (assocSeq == + * null) { SequenceIdMatcher idm = new SequenceIdMatcher(viewport + * .getAlignment().getSequencesArray()); if (pdbfn.length() > 0) { + * // attempt to find a match in the alignment SequenceI mtch = + * idm.findIdMatch(pdbfn); int l = 0, c = pdbfn.indexOf("."); while + * (mtch == null && c != -1) { while ((c = pdbfn.indexOf(".", l)) > + * l) { l = c; } if (l > -1) { pdbfn = pdbfn.substring(0, l); } mtch + * = idm.findIdMatch(pdbfn); } if (mtch != null) { // try and + * associate // prompt ? PDBEntry pe = new AssociatePdbFileWithSeq() + * .associatePdbWithSeq(file, protocol, mtch, true); if (pe != null) + * { System.err.println("Associated file : " + file + " with " + + * mtch.getDisplayId(true)); alignPanel.paintAlignment(true); } } // + * TODO: maybe need to load as normal otherwise return; } } + */ + // try to parse it as a features file + boolean isGroupsFile = parseFeaturesFile(file, protocol); + // if it wasn't a features file then we just treat it as a general + // alignment file to load into the current view. + if (!isGroupsFile) + { + new FileLoader().LoadFile(viewport, file, protocol, format); + } + else + { + alignPanel.paintAlignment(true); + } } } } @@ -4884,6 +4978,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void tabSelectionChanged(int index) { if (index > -1) @@ -4894,6 +4989,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } + @Override public void tabbedPane_mousePressed(MouseEvent e) { if (SwingUtilities.isRightMouseButton(e)) @@ -4918,6 +5014,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Open the dialog for regex description parsing. */ + @Override protected void extractScores_actionPerformed(ActionEvent e) { ParseProperties pp = new jalview.analysis.ParseProperties( @@ -4935,11 +5032,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent * ) */ + @Override protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); @@ -4947,10 +5045,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. * ActionEvent) */ + @Override protected void showNpFeats_actionPerformed(ActionEvent e) { viewport.setShowNpFeats(showNpFeatsMenuitem.isSelected()); @@ -4959,7 +5058,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * find the viewport amongst the tabs in this alignment frame and close that * tab - * + * * @param av */ public boolean closeView(AlignViewport av) @@ -5000,11 +5099,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av @@ -5020,12 +5121,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, final AlignFrame me = this; new Thread(new Runnable() { + @Override public void run() { final jalview.ws.SequenceFetcher sf = SequenceFetcher .getSequenceFetcherSingleton(me); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { String[] dbclasses = sf.getOrderedSupportedSources(); @@ -5066,11 +5169,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av @@ -5098,11 +5203,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, + "'"); fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av @@ -5143,11 +5250,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, fetchr.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { new Thread(new Runnable() { + @Override public void run() { new jalview.ws.DBRefFetcher(alignPanel.av @@ -5195,6 +5304,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Left justify the whole alignment. */ + @Override protected void justifyLeftMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -5205,6 +5315,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * Right justify the whole alignment. */ + @Override protected void justifyRightMenuItem_actionPerformed(ActionEvent e) { AlignmentI al = viewport.getAlignment(); @@ -5220,11 +5331,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java. * awt.event.ActionEvent) */ + @Override protected void showUnconservedMenuItem_actionPerformed(ActionEvent e) { viewport.setShowUnconserved(showNonconservedMenuItem.getState()); @@ -5233,11 +5345,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event * .ActionEvent) */ + @Override protected void showGroupConsensus_actionPerformed(ActionEvent e) { viewport.setShowGroupConsensus(showGroupConsensus.getState()); @@ -5247,11 +5360,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showGroupConservation_actionPerformed(ActionEvent e) { viewport.setShowGroupConservation(showGroupConservation.getState()); @@ -5260,11 +5374,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showConsensusHistogram_actionPerformed(ActionEvent e) { viewport.setShowConsensusHistogram(showConsensusHistogram.getState()); @@ -5273,23 +5388,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void showSequenceLogo_actionPerformed(ActionEvent e) { viewport.setShowSequenceLogo(showSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + @Override protected void normaliseSequenceLogo_actionPerformed(ActionEvent e) { viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState()); alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); } + @Override protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e) { alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState()); @@ -5297,11 +5415,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /* * (non-Javadoc) - * + * * @see * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt * .event.ActionEvent) */ + @Override protected void makeGrpsFromSelection_actionPerformed(ActionEvent e) { if (viewport.getSelectionGroup() != null) @@ -5323,9 +5442,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, Color col = new Color((int) (Math.random() * 255), (int) (Math.random() * 255), (int) (Math.random() * 255)); col = col.brighter(); - for (Enumeration sq = gps[g].getSequences(null).elements(); sq - .hasMoreElements(); viewport.setSequenceColour( - (SequenceI) sq.nextElement(), col)) + for (SequenceI s:gps[g].getSequences()) + viewport.setSequenceColour( + s, col) ; } PaintRefresher.Refresh(this, viewport.getSequenceSetId()); @@ -5336,7 +5455,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * make the given alignmentPanel the currently selected tab - * + * * @param alignmentPanel */ public void setDisplayedView(AlignmentPanel alignmentPanel) @@ -5367,6 +5486,7 @@ class PrintThread extends Thread static PageFormat pf; + @Override public void run() { PrinterJob printJob = PrinterJob.getPrinterJob();