From 239ea1f6501b7a04d4e80149690c16e81560c00f Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 9 Jun 2009 15:16:59 +0000 Subject: [PATCH] fix null pointer when new view is created then closed after a vamsas sync of stored views --- src/jalview/gui/AlignFrame.java | 414 ++++++++++++++++++++++----------------- 1 file changed, 239 insertions(+), 175 deletions(-) diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2ee643f..d8459a9 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -81,51 +81,66 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { this(al, null, width, height); } + /** - * Creates a new AlignFrame object with specific width, height and sequenceSetId + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * * @param al * @param width * @param height * @param sequenceSetId */ - public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId) + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId) { this(al, null, width, height, sequenceSetId); } + /** - * Creates a new AlignFrame object with specific width, height and sequenceSetId + * Creates a new AlignFrame object with specific width, height and + * sequenceSetId + * * @param al * @param width * @param height * @param sequenceSetId * @param viewId */ - public AlignFrame(AlignmentI al, int width, int height, String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, int width, int height, + String sequenceSetId, String viewId) { this(al, null, width, height, sequenceSetId, viewId); } + /** * new alignment window with hidden columns * * @param al - * AlignmentI + * AlignmentI * @param hiddenColumns - * ColumnSelection or null - * @param width Width of alignment frame - * @param height height of frame. + * ColumnSelection or null + * @param width + * Width of alignment frame + * @param height + * height of frame. */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height) { this(al, hiddenColumns, width, height, null); } + /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * * @param al * @param hiddenColumns * @param width * @param height - * @param sequenceSetId (may be null) + * @param sequenceSetId + * (may be null) */ public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, String sequenceSetId) @@ -134,16 +149,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * Create alignment frame for al with hiddenColumns, a specific width and height, and specific sequenceId + * Create alignment frame for al with hiddenColumns, a specific width and + * height, and specific sequenceId + * * @param al * @param hiddenColumns * @param width * @param height - * @param sequenceSetId (may be null) - * @param viewId (may be null) + * @param sequenceSetId + * (may be null) + * @param viewId + * (may be null) */ - public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, int width, int height, - String sequenceSetId, String viewId) + public AlignFrame(AlignmentI al, ColumnSelection hiddenColumns, + int width, int height, String sequenceSetId, String viewId) { setSize(width, height); viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId); @@ -163,9 +182,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Make a new AlignFrame from exisiting alignmentPanels * * @param ap - * AlignmentPanel + * AlignmentPanel * @param av - * AlignViewport + * AlignViewport */ public AlignFrame(AlignmentPanel ap) { @@ -174,8 +193,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addAlignmentPanel(ap, false); init(); } + /** - * initalise the alignframe from the underlying viewport data and the configurations + * initalise the alignframe from the underlying viewport data and the + * configurations */ void init() { @@ -229,9 +250,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * button functionality. * * @param file - * valid filename + * valid filename * @param format - * format of file + * format of file */ public void setFileName(String file, String format) { @@ -581,7 +602,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * loading from Jalview2XML.java * * @param av - * AlignViewport + * AlignViewport */ void setMenusFromViewport(AlignViewport av) { @@ -644,7 +665,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } if (progressBarHandlers.contains(new Long(id))) { - progressBarHandlers.remove(new Long(id)); + progressBarHandlers.remove(new Long(id)); } layout.setRows(layout.getRows() - 1); } @@ -667,29 +688,35 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, setMenusForViewport(); validate(); } - public void registerHandler(final long id, final IProgressIndicatorHandler handler) + + public void registerHandler(final long id, + final IProgressIndicatorHandler handler) { - if (progressBarHandlers==null || !progressBars.contains(new Long(id))) + if (progressBarHandlers == null || !progressBars.contains(new Long(id))) { - throw new Error("call setProgressBar before registering the progress bar's handler."); + throw new Error( + "call setProgressBar before registering the progress bar's handler."); } progressBarHandlers.put(new Long(id), handler); final JPanel progressPanel = (JPanel) progressBars.get(new Long(id)); if (handler.canCancel()) { JButton cancel = new JButton("Cancel"); - final IProgressIndicator us=this; - cancel.addActionListener(new ActionListener() { + final IProgressIndicator us = this; + cancel.addActionListener(new ActionListener() + { public void actionPerformed(ActionEvent e) { handler.cancelActivity(id); - us.setProgressBar("Cancelled "+((JLabel)progressPanel.getComponent(0)).getText(), id); + us.setProgressBar("Cancelled " + + ((JLabel) progressPanel.getComponent(0)).getText(), id); } }); progressPanel.add(cancel, BorderLayout.EAST); } } + /** * * @return true if any progress bars are still active @@ -783,8 +810,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, public void save_actionPerformed(ActionEvent e) { if (fileName == null - || (currentFileFormat == null - || !jalview.io.FormatAdapter.isValidIOFormat(currentFileFormat, true)) + || (currentFileFormat == null || !jalview.io.FormatAdapter + .isValidIOFormat(currentFileFormat, true)) || fileName.startsWith("http")) { saveAs_actionPerformed(null); @@ -799,7 +826,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void saveAs_actionPerformed(ActionEvent e) { @@ -936,7 +963,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void outputText_actionPerformed(ActionEvent e) { @@ -972,7 +999,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void htmlMenuItem_actionPerformed(ActionEvent e) { @@ -990,7 +1017,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createPNG(File f) { @@ -1001,7 +1028,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void createEPS(File f) { @@ -1018,7 +1045,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void printMenuItem_actionPerformed(ActionEvent e) { @@ -1062,10 +1089,10 @@ 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. + * 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 + * @param closeAllTabs */ public void closeMenuItem_actionPerformed(boolean closeAllTabs) { @@ -1080,16 +1107,20 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { if (closeAllTabs) { - for (int i = 0; i < alignPanels.size(); i++) + if (this.isClosed()) { - AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); - ap.closePanel(); + // really close all the windows - otherwise wait till + // setClosed(true) is called + for (int i = 0; i < alignPanels.size(); i++) + { + AlignmentPanel ap = (AlignmentPanel) alignPanels.elementAt(i); + ap.closePanel(); + } } } else { closeView(alignPanel); - viewport = null; } } @@ -1105,6 +1136,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, /** * close alignPanel2 and shuffle tabs appropriately. + * * @param alignPanel2 */ public void closeView(AlignmentPanel alignPanel2) @@ -1112,14 +1144,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, int index = tabbedPane.getSelectedIndex(); int closedindex = tabbedPane.indexOfComponent(alignPanel2); alignPanels.removeElement(alignPanel2); - - if (viewport == alignPanel2.av) - { - viewport = null; - } + // Unnecessary + // if (viewport == alignPanel2.av) + // { + // viewport = null; + // } alignPanel2.closePanel(); alignPanel2 = null; - + tabbedPane.removeTabAt(closedindex); tabbedPane.validate(); @@ -1129,7 +1161,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, index--; } - this.tabSelectionChanged(index); + this.tabSelectionChanged(index); } /** @@ -1203,7 +1235,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void undoMenuItem_actionPerformed(ActionEvent e) { @@ -1228,7 +1260,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void redoMenuItem_actionPerformed(ActionEvent e) { @@ -1298,7 +1330,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param up - * DOCUMENT ME! + * DOCUMENT ME! */ public void moveSelectedSequences(boolean up) { @@ -1445,7 +1477,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void copy_actionPerformed(ActionEvent e) { @@ -1510,7 +1542,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void pasteNew_actionPerformed(ActionEvent e) { @@ -1521,7 +1553,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void pasteThis_actionPerformed(ActionEvent e) { @@ -1532,7 +1564,7 @@ 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. + * true to paste to a new alignment, otherwise add to this. */ void paste(boolean newAlignment) { @@ -1801,7 +1833,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void cut_actionPerformed(ActionEvent e) { @@ -1813,7 +1845,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void delete_actionPerformed(ActionEvent evt) { @@ -1873,7 +1905,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void deleteGroups_actionPerformed(ActionEvent e) { @@ -1888,7 +1920,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1910,7 +1942,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1932,7 +1964,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void invertSequenceMenuItem_actionPerformed(ActionEvent e) { @@ -1965,7 +1997,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void remove2LeftMenuItem_actionPerformed(ActionEvent e) { @@ -1976,7 +2008,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void remove2RightMenuItem_actionPerformed(ActionEvent e) { @@ -2053,7 +2085,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) { @@ -2099,7 +2131,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2137,7 +2169,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void padGapsMenuitem_actionPerformed(ActionEvent e) { @@ -2145,21 +2177,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.firePropertyChange("alignment", null, viewport.getAlignment() .getSequences()); } - - //else + + // else { // if (justifySeqs>0) { // alignment.justify(justifySeqs!=RIGHT_JUSTIFY); } } - //} - + + // } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void findMenuItem_actionPerformed(ActionEvent e) { @@ -2229,7 +2262,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void font_actionPerformed(ActionEvent e) { @@ -2240,7 +2273,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void seqLimit_actionPerformed(ActionEvent e) { @@ -2262,14 +2295,18 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, viewport.centreColumnLabels = centreColumnLabelsMenuItem.getState(); alignPanel.paintAlignment(true); } - /* (non-Javadoc) + + /* + * (non-Javadoc) + * * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed() */ protected void followHighlight_actionPerformed() { if (viewport.followHighlight = this.followHighlightMenuItem.getState()) { - alignPanel.scrollToPosition(alignPanel.seqPanel.seqCanvas.searchResults, false); + alignPanel.scrollToPosition( + alignPanel.seqPanel.seqCanvas.searchResults, false); } } @@ -2277,7 +2314,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void colourTextMenuItem_actionPerformed(ActionEvent e) { @@ -2289,7 +2326,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void wrapMenuItem_actionPerformed(ActionEvent e) { @@ -2333,7 +2370,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleAbove_actionPerformed(ActionEvent e) { @@ -2345,7 +2382,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleLeft_actionPerformed(ActionEvent e) { @@ -2357,7 +2394,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void scaleRight_actionPerformed(ActionEvent e) { @@ -2369,7 +2406,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void viewBoxesMenuItem_actionPerformed(ActionEvent e) { @@ -2381,7 +2418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void viewTextMenuItem_actionPerformed(ActionEvent e) { @@ -2393,7 +2430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void renderGapsMenuItem_actionPerformed(ActionEvent e) { @@ -2417,7 +2454,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Set or clear 'Show Sequence Features' * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void showSeqFeatures_actionPerformed(ActionEvent evt) { @@ -2428,15 +2465,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.getOverviewPanel().updateOverviewImage(); } } + /** * Set or clear 'Show Sequence Features' * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void showSeqFeaturesHeight_actionPerformed(ActionEvent evt) { - viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight.isSelected()); + viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight + .isSelected()); if (viewport.getShowSequenceFeaturesHeight()) { // ensure we're actually displaying features @@ -2454,7 +2493,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void annotationPanelMenuItem_actionPerformed(ActionEvent e) { @@ -2529,7 +2568,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void overviewMenuItem_actionPerformed(ActionEvent e) { @@ -2567,7 +2606,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void noColourmenuItem_actionPerformed(ActionEvent e) { @@ -2578,7 +2617,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void clustalColour_actionPerformed(ActionEvent e) { @@ -2591,7 +2630,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void zappoColour_actionPerformed(ActionEvent e) { @@ -2602,7 +2641,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void taylorColour_actionPerformed(ActionEvent e) { @@ -2613,7 +2652,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void hydrophobicityColour_actionPerformed(ActionEvent e) { @@ -2624,7 +2663,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void helixColour_actionPerformed(ActionEvent e) { @@ -2635,7 +2674,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void strandColour_actionPerformed(ActionEvent e) { @@ -2646,7 +2685,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void turnColour_actionPerformed(ActionEvent e) { @@ -2657,7 +2696,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void buriedColour_actionPerformed(ActionEvent e) { @@ -2668,7 +2707,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void nucleotideColour_actionPerformed(ActionEvent e) { @@ -2684,7 +2723,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void applyToAllGroups_actionPerformed(ActionEvent e) { @@ -2695,7 +2734,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param cs - * DOCUMENT ME! + * DOCUMENT ME! */ public void changeColour(ColourSchemeI cs) { @@ -2820,7 +2859,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void modifyPID_actionPerformed(ActionEvent e) { @@ -2837,7 +2876,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void modifyConservation_actionPerformed(ActionEvent e) { @@ -2854,7 +2893,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void conservationMenuItem_actionPerformed(ActionEvent e) { @@ -2872,7 +2911,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void abovePIDThreshold_actionPerformed(ActionEvent e) { @@ -2890,7 +2929,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void userDefinedColour_actionPerformed(ActionEvent e) { @@ -2983,7 +3022,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void PIDColour_actionPerformed(ActionEvent e) { @@ -2994,7 +3033,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void BLOSUM62Colour_actionPerformed(ActionEvent e) { @@ -3005,7 +3044,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) { @@ -3021,7 +3060,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortIDMenuItem_actionPerformed(ActionEvent e) { @@ -3030,17 +3069,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, addHistoryItem(new OrderCommand("ID Sort", oldOrder, viewport.alignment)); alignPanel.paintAlignment(true); } + /** * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortLengthMenuItem_actionPerformed(ActionEvent e) { SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByLength(viewport.getAlignment()); - addHistoryItem(new OrderCommand("Length Sort", oldOrder, viewport.alignment)); + addHistoryItem(new OrderCommand("Length Sort", oldOrder, + viewport.alignment)); alignPanel.paintAlignment(true); } @@ -3048,7 +3089,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void sortGroupMenuItem_actionPerformed(ActionEvent e) { @@ -3064,7 +3105,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) { @@ -3075,7 +3116,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e) { @@ -3098,7 +3139,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void PCAMenuItem_actionPerformed(ActionEvent e) { @@ -3133,7 +3174,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) { @@ -3144,7 +3185,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) { @@ -3155,7 +3196,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -3166,7 +3207,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) { @@ -3177,11 +3218,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param type - * DOCUMENT ME! + * DOCUMENT ME! * @param pwType - * DOCUMENT ME! + * DOCUMENT ME! * @param title - * DOCUMENT ME! + * DOCUMENT ME! */ void NewTreePanel(String type, String pwType, String title) { @@ -3265,9 +3306,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param title - * DOCUMENT ME! + * DOCUMENT ME! * @param order - * DOCUMENT ME! + * DOCUMENT ME! */ public void addSortByOrderMenuItem(String title, final AlignmentOrder order) @@ -3296,10 +3337,10 @@ 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 + * the menu to add the option to * @param scoreLabel - * the label used to retrieve scores for each sequence on the - * alignment + * the label used to retrieve scores for each sequence on the + * alignment */ public void addSortByAnnotScoreMenuItem(JMenu sort, final String scoreLabel) @@ -3379,9 +3420,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * modified. * * @param treePanel - * Displayed tree window. + * Displayed tree window. * @param title - * SortBy menu item title. + * SortBy menu item title. */ public void buildTreeMenu() { @@ -3508,7 +3549,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ protected void LoadtreeMenuItem_actionPerformed(ActionEvent e) { @@ -3567,19 +3608,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * current alignment view * * @param nf - * the tree + * the tree * @param title - * tree viewer title + * tree viewer title * @param input - * Associated alignment input data (or null) + * Associated alignment input data (or null) * @param w - * width + * width * @param h - * height + * height * @param x - * position + * position * @param y - * position + * position * @return TreePanel handle */ public TreePanel ShowNewickTree(NewickFile nf, String title, @@ -3757,9 +3798,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, showProducts.removeAll(); final boolean dna = viewport.getAlignment().isNucleotide(); final Alignment ds = dataset; - String[] ptypes = (selection==null || selection.length==0) ? null - : CrossRef.findSequenceXrefTypes(dna, selection, - dataset); + String[] ptypes = (selection == null || selection.length == 0) ? null + : CrossRef.findSequenceXrefTypes(dna, selection, dataset); // Object[] prods = // CrossRef.buildXProductsList(viewport.getAlignment().isNucleotide(), // selection, dataset, true); @@ -3965,9 +4005,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * Try to load a features file onto the alignment. * * @param file - * contents or path to retrieve file + * contents or path to retrieve file * @param type - * access mode of file (see jalview.io.AlignFile) + * access mode of file (see jalview.io.AlignFile) * @return true if features file was parsed corectly. */ public boolean parseFeaturesFile(String file, String type) @@ -3987,7 +4027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.showSequenceFeatures = true; showSeqFeatures.setSelected(true); - if (alignPanel.seqPanel.seqCanvas.fr!=null) + if (alignPanel.seqPanel.seqCanvas.fr != null) { // update the min/max ranges where necessary alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true); @@ -4078,7 +4118,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * AlignFrame. * * @param file - * either a filename or a URL string. + * either a filename or a URL string. */ public void loadJalviewDataFile(String file) { @@ -4186,16 +4226,23 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @see + * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent + * ) */ protected void showDbRefs_actionPerformed(ActionEvent e) { viewport.setShowDbRefs(showDbRefsMenuitem.isSelected()); } - /* (non-Javadoc) - * @see jalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.ActionEvent) + /* + * (non-Javadoc) + * + * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event. + * ActionEvent) */ protected void showNpFeats_actionPerformed(ActionEvent e) { @@ -4203,7 +4250,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, } /** - * find the viewport amongst the tabs in this alignment frame and close that tab + * find the viewport amongst the tabs in this alignment frame and close that + * tab + * * @param av */ public boolean closeView(AlignViewport av) @@ -4214,7 +4263,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return true; } Component[] comp = tabbedPane.getComponents(); - for (int i=0;comp!=null && i0) + int comp = 0, mcomp = 15; + String mname = null; + if (otherdb != null && otherdb.length > 0) { - for (int i=0; i