X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=57a09ef9d71b4f259b757755633948edabbbdf8d;hb=6cfc81d62c929df5f7dd70b3048e5e5dced1429a;hp=91de052f16bb0d22d3dfc128415c0cdaee24930c;hpb=4b3b10e22e7c22b9cfaecbd831e1e6bb9ba539a2;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 91de052..57a09ef 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -1,6 +1,6 @@ /* * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU General Public License @@ -19,20 +19,21 @@ package jalview.appletgui; -import jalview.schemes.*; -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.io.*; -import jalview.commands.*; +import java.io.*; +import java.net.*; +import java.util.*; + import java.awt.*; import java.awt.event.*; -import java.util.*; -import java.io.InputStreamReader; -import java.io.BufferedReader; -import java.net.URL; +import jalview.analysis.*; +import jalview.commands.*; +import jalview.datamodel.*; +import jalview.io.*; +import jalview.schemes.*; -public class AlignFrame extends Frame implements ActionListener, +public class AlignFrame + extends Frame implements ActionListener, ItemListener, KeyListener, MouseListener { public AlignmentPanel alignPanel; @@ -42,18 +43,22 @@ public class AlignFrame extends Frame implements ActionListener, String jalviewServletURL; - - public AlignFrame(AlignmentI al, - jalview.bin.JalviewLite applet, - String title, - boolean embedded) + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) { - jalviewServletURL = applet.getParameter("APPLICATION_URL"); + if (applet != null) + { + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + } - try{ + try + { jbInit(); - }catch(Exception ex) + } + catch (Exception ex) { ex.printStackTrace(); } @@ -68,15 +73,19 @@ public class AlignFrame extends Frame implements ActionListener, seqLimits.setState(viewport.showJVSuffix); - if(applet!=null) + if (applet != null) { String param = applet.getParameter("sortBy"); if (param != null) { if (param.equalsIgnoreCase("Id")) + { sortIDMenuItem_actionPerformed(); + } else if (param.equalsIgnoreCase("Pairwise Identity")) + { sortPairwiseMenuItem_actionPerformed(); + } } param = applet.getParameter("wrap"); @@ -109,28 +118,28 @@ public class AlignFrame extends Frame implements ActionListener, } - //Some JVMS send keyevents to Top frame or lowest panel, - //Havent worked out why yet. So add to both this frame and seqCanvas for now - this.addKeyListener(this); - alignPanel.seqPanel.seqCanvas.addKeyListener(this); - alignPanel.idPanel.idCanvas.addKeyListener(this); - alignPanel.scalePanel.addKeyListener(this); - alignPanel.annotationPanel.addKeyListener(this); + //Some JVMS send keyevents to Top frame or lowest panel, + //Havent worked out why yet. So add to both this frame and seqCanvas for now + this.addKeyListener(this); + alignPanel.seqPanel.seqCanvas.addKeyListener(this); + alignPanel.idPanel.idCanvas.addKeyListener(this); + alignPanel.scalePanel.addKeyListener(this); + alignPanel.annotationPanel.addKeyListener(this); - - if(embedded) - { - setEmbedded(); - } - else - { - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, - DEFAULT_HEIGHT); - } - alignPanel.validate(); - alignPanel.repaint(); + if (embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH, + DEFAULT_HEIGHT); + } + alignPanel.validate(); + alignPanel.paintAlignment(true); } + public AlignViewport getAlignViewport() { return viewport; @@ -141,7 +150,6 @@ public class AlignFrame extends Frame implements ActionListener, return alignPanel.seqPanel.seqCanvas; } - /** * DOCUMENT ME! * @@ -152,39 +160,46 @@ public class AlignFrame extends Frame implements ActionListener, { Hashtable featureLinks = new Hashtable(); boolean featuresFile = false; - try{ - featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport.alignment, - alignPanel.seqPanel.seqCanvas. - getFeatureRenderer().featureColours, - featureLinks, - true); + try + { + featuresFile = new jalview.io.FeaturesFile(file, + type).parse(viewport.alignment, + alignPanel.seqPanel.seqCanvas. + getFeatureRenderer().featureColours, + featureLinks, + true); } - catch(Exception ex) + catch (Exception ex) { ex.printStackTrace(); } - if(featuresFile) + if (featuresFile) { - if(featureLinks.size()>0) + if (featureLinks.size() > 0) + { alignPanel.seqPanel.seqCanvas .getFeatureRenderer().featureLinks = featureLinks; + } viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } } - public void keyPressed(KeyEvent evt) { - if (viewport.cursorMode - && evt.getKeyCode() >= KeyEvent.VK_0 - && evt.getKeyCode() <= KeyEvent.VK_9) - { - alignPanel.seqPanel.numberPressed(evt.getKeyChar()); - } + if (viewport.cursorMode && + ( (evt.getKeyCode() >= KeyEvent.VK_0 && + evt.getKeyCode() <= KeyEvent.VK_9) + || + (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 && + evt.getKeyCode() <= KeyEvent.VK_NUMPAD9) + ) + && Character.isDigit(evt.getKeyChar())) + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + switch (evt.getKeyCode()) { @@ -220,38 +235,45 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - if(viewport.cursorMode) + if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0,1); + alignPanel.seqPanel.moveCursor(0, 1); } else + { moveSelectedSequences(false); + } break; case KeyEvent.VK_UP: if (viewport.cursorMode) { - alignPanel.seqPanel.moveCursor(0,-1); + alignPanel.seqPanel.moveCursor(0, -1); } else + { moveSelectedSequences(true); + } break; case KeyEvent.VK_LEFT: - if(viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(-1,0); - } + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(false, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( -1, 0); break; case KeyEvent.VK_RIGHT: - if (viewport.cursorMode) - { - alignPanel.seqPanel.moveCursor(1,0); - } - break; + if (evt.isAltDown() || !viewport.cursorMode) + slideSequences(true, + alignPanel.seqPanel.getKeyboardNo1()); + else + alignPanel.seqPanel.moveCursor( 1, 0); + break; + case KeyEvent.VK_SPACE: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() || evt.isShiftDown() @@ -262,13 +284,13 @@ public class AlignFrame extends Frame implements ActionListener, case KeyEvent.VK_DELETE: case KeyEvent.VK_BACK_SPACE: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() || evt.isShiftDown() || evt.isAltDown()); } - else + else { cut_actionPerformed(); alignPanel.seqPanel.seqCanvas.repaint(); @@ -276,13 +298,13 @@ public class AlignFrame extends Frame implements ActionListener, break; case KeyEvent.VK_S: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRow(); } break; case KeyEvent.VK_P: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorPosition(); } @@ -290,35 +312,35 @@ public class AlignFrame extends Frame implements ActionListener, case KeyEvent.VK_ENTER: case KeyEvent.VK_COMMA: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setCursorRowAndColumn(); } break; case KeyEvent.VK_Q: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(true); } break; case KeyEvent.VK_M: - if(viewport.cursorMode) + if (viewport.cursorMode) { alignPanel.seqPanel.setSelectionAreaAtCursor(false); } break; - case KeyEvent.VK_F2: - viewport.cursorMode = ! viewport.cursorMode; - statusBar.setText("Keyboard editing mode is "+ - (viewport.cursorMode ? "on" : "off")); - if(viewport.cursorMode) - { - alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; - alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; - } - break; + case KeyEvent.VK_F2: + viewport.cursorMode = !viewport.cursorMode; + statusBar.setText("Keyboard editing mode is " + + (viewport.cursorMode ? "on" : "off")); + if (viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + break; case KeyEvent.VK_F: if (evt.isControlDown()) @@ -334,47 +356,61 @@ public class AlignFrame extends Frame implements ActionListener, boolean hide = false; SequenceGroup sg = viewport.getSelectionGroup(); - if(toggleSeqs) + if (toggleSeqs) { - if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) { hide = true; viewport.hideAllSelectedSeqs(); } - else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + else if (! (toggleCols && viewport.colSel.getSelected().size() > 0)) + { viewport.showAllHiddenSeqs(); + } } - if(toggleCols) + if (toggleCols) { if (viewport.colSel.getSelected().size() > 0) { viewport.hideSelectedColumns(); - if(!toggleSeqs) - viewport.selectionGroup = sg; + if (!toggleSeqs) + { + viewport.selectionGroup = sg; + } } else if (!hide) + { viewport.showAllHiddenColumns(); + } } break; } case KeyEvent.VK_PAGE_UP: if (viewport.wrapAlignment) + { alignPanel.scrollUp(true); + } else + { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq - viewport.endSeq + viewport.startSeq); + } break; case KeyEvent.VK_PAGE_DOWN: if (viewport.wrapAlignment) + { alignPanel.scrollUp(false); + } else + { alignPanel.setScrollValues(viewport.startRes, viewport.startSeq + viewport.endSeq - viewport.startSeq); + } break; case KeyEvent.VK_Z: @@ -409,18 +445,26 @@ public class AlignFrame extends Frame implements ActionListener, if (evt.isControlDown()) { if (evt.isShiftDown()) + { this.removeAllGapsMenuItem_actionPerformed(); + } else + { removeGappedColumnMenuItem_actionPerformed(); + } } break; case KeyEvent.VK_I: if (evt.isControlDown()) { if (evt.isAltDown()) + { viewport.invertColumnSelection(); + } else + { this.invertSequenceMenuItem_actionPerformed(); + } } break; @@ -429,207 +473,364 @@ public class AlignFrame extends Frame implements ActionListener, { this.deleteGroups_actionPerformed(); } - break; - - case KeyEvent.VK_T: - if (evt.isControlDown()) - { - newView(); - } - break; + break; + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; - } - alignPanel.repaint(); + } + alignPanel.paintAlignment(true); } + public void keyReleased(KeyEvent evt) {} + public void keyTyped(KeyEvent evt) {} -public void itemStateChanged(ItemEvent evt) - { - if(evt.getSource()==colourTextMenuItem) - colourTextMenuItem_actionPerformed(); - else if(evt.getSource()==wrapMenuItem) - wrapMenuItem_actionPerformed(); - else if(evt.getSource()==scaleAbove) - viewport.setScaleAboveWrapped(scaleAbove.getState()); - else if(evt.getSource()==scaleLeft) - viewport.setScaleLeftWrapped(scaleLeft.getState()); - else if(evt.getSource()==scaleRight) - viewport.setScaleRightWrapped(scaleRight.getState()); - else if(evt.getSource()==seqLimits) + public void itemStateChanged(ItemEvent evt) + { + if (evt.getSource() == colourTextMenuItem) + { + colourTextMenuItem_actionPerformed(); + } + else if (evt.getSource() == wrapMenuItem) + { + wrapMenuItem_actionPerformed(); + } + else if (evt.getSource() == scaleAbove) + { + viewport.setScaleAboveWrapped(scaleAbove.getState()); + } + else if (evt.getSource() == scaleLeft) + { + viewport.setScaleLeftWrapped(scaleLeft.getState()); + } + else if (evt.getSource() == scaleRight) + { + viewport.setScaleRightWrapped(scaleRight.getState()); + } + else if (evt.getSource() == seqLimits) + { seqLimits_itemStateChanged(); - else if(evt.getSource()==viewBoxesMenuItem) - viewport.setShowBoxes(viewBoxesMenuItem.getState()); - else if(evt.getSource()==viewTextMenuItem) - viewport.setShowText(viewTextMenuItem.getState()); - else if(evt.getSource()==renderGapsMenuItem) - viewport.setRenderGaps(renderGapsMenuItem.getState()); - else if(evt.getSource()==annotationPanelMenuItem) + } + else if (evt.getSource() == viewBoxesMenuItem) + { + viewport.setShowBoxes(viewBoxesMenuItem.getState()); + } + else if (evt.getSource() == viewTextMenuItem) + { + viewport.setShowText(viewTextMenuItem.getState()); + } + else if (evt.getSource() == renderGapsMenuItem) + { + viewport.setRenderGaps(renderGapsMenuItem.getState()); + } + else if (evt.getSource() == annotationPanelMenuItem) { viewport.setShowAnnotation(annotationPanelMenuItem.getState()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); } - else if(evt.getSource()==sequenceFeatures) - { - viewport.showSequenceFeatures(sequenceFeatures.getState()); - alignPanel.seqPanel.seqCanvas.repaint(); - } - else if(evt.getSource()==conservationMenuItem) - conservationMenuItem_actionPerformed(); - else if(evt.getSource()==abovePIDThreshold) - abovePIDThreshold_actionPerformed(); - else if(evt.getSource()==applyToAllGroups) - viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); - else if(evt.getSource()==autoCalculate) - viewport.autocalculateConsensus = autoCalculate.getState(); - - alignPanel.repaint(); - } - public void actionPerformed(ActionEvent evt) - { + else if (evt.getSource() == sequenceFeatures) + { + viewport.showSequenceFeatures(sequenceFeatures.getState()); + alignPanel.seqPanel.seqCanvas.repaint(); + } + else if (evt.getSource() == conservationMenuItem) + { + conservationMenuItem_actionPerformed(); + } + else if (evt.getSource() == abovePIDThreshold) + { + abovePIDThreshold_actionPerformed(); + } + else if (evt.getSource() == applyToAllGroups) + { + viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); + } + else if (evt.getSource() == autoCalculate) + { + viewport.autocalculateConsensus = autoCalculate.getState(); + } + + alignPanel.paintAlignment(true); + } + + public void actionPerformed(ActionEvent evt) + { Object source = evt.getSource(); - if(source==inputText) + if (source == inputText) + { inputText_actionPerformed(); - else if(source==loadTree) + } + else if (source == loadTree) + { loadTree_actionPerformed(); - else if(source==loadApplication) + } + else if (source == loadApplication) + { launchFullApplication(); - else if(source==closeMenuItem) + } + else if (source == loadAnnotations) + { + loadAnnotations(); + } + else if (source == outputAnnotations) + { + outputAnnotations(true); + } + else if (source == outputFeatures) + { + outputFeatures(true, "Jalview"); + } + else if (source == closeMenuItem) + { closeMenuItem_actionPerformed(); - else if(source==copy) + } + else if (source == copy) + { copy_actionPerformed(); - else if(source==undoMenuItem) + } + else if (source == undoMenuItem) + { undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) + } + else if (source == redoMenuItem) + { redoMenuItem_actionPerformed(); - else if(source==inputText) - inputText_actionPerformed(); - else if(source==closeMenuItem) - closeMenuItem_actionPerformed(); - else if(source==undoMenuItem) - undoMenuItem_actionPerformed(); - else if(source==redoMenuItem) - redoMenuItem_actionPerformed(); - else if(source==copy) - copy_actionPerformed(); - else if(source==pasteNew) - pasteNew_actionPerformed(); - else if(source==pasteThis) - pasteThis_actionPerformed(); - else if(source==cut) - cut_actionPerformed(); - else if(source==delete) - delete_actionPerformed(); - else if(source==deleteGroups) - deleteGroups_actionPerformed(); - else if(source==selectAllSequenceMenuItem) - selectAllSequenceMenuItem_actionPerformed(); - else if(source==deselectAllSequenceMenuItem) - deselectAllSequenceMenuItem_actionPerformed(); - else if(source==invertSequenceMenuItem) - invertSequenceMenuItem_actionPerformed(); - else if(source==invertColSel) - { viewport.invertColumnSelection(); alignPanel.repaint(); } - else if(source==remove2LeftMenuItem) - trimAlignment(true); - else if(source==remove2RightMenuItem) - trimAlignment(false); - else if(source==removeGappedColumnMenuItem) - removeGappedColumnMenuItem_actionPerformed(); - else if(source==removeAllGapsMenuItem) - removeAllGapsMenuItem_actionPerformed(); - else if(source==findMenuItem) - findMenuItem_actionPerformed(); - else if(source==font) - new FontChooser(alignPanel); + } + else if (source == inputText) + { + inputText_actionPerformed(); + } + else if (source == closeMenuItem) + { + closeMenuItem_actionPerformed(); + } + else if (source == undoMenuItem) + { + undoMenuItem_actionPerformed(); + } + else if (source == redoMenuItem) + { + redoMenuItem_actionPerformed(); + } + else if (source == copy) + { + copy_actionPerformed(); + } + else if (source == pasteNew) + { + pasteNew_actionPerformed(); + } + else if (source == pasteThis) + { + pasteThis_actionPerformed(); + } + else if (source == cut) + { + cut_actionPerformed(); + } + else if (source == delete) + { + delete_actionPerformed(); + } + else if (source == deleteGroups) + { + deleteGroups_actionPerformed(); + } + else if (source == selectAllSequenceMenuItem) + { + selectAllSequenceMenuItem_actionPerformed(); + } + else if (source == deselectAllSequenceMenuItem) + { + deselectAllSequenceMenuItem_actionPerformed(); + } + else if (source == invertSequenceMenuItem) + { + invertSequenceMenuItem_actionPerformed(); + } + else if (source == invertColSel) + { + viewport.invertColumnSelection(); + alignPanel.paintAlignment(true); + } + else if (source == remove2LeftMenuItem) + { + trimAlignment(true); + } + else if (source == remove2RightMenuItem) + { + trimAlignment(false); + } + else if (source == removeGappedColumnMenuItem) + { + removeGappedColumnMenuItem_actionPerformed(); + } + else if (source == removeAllGapsMenuItem) + { + removeAllGapsMenuItem_actionPerformed(); + } + else if (source == findMenuItem) + { + findMenuItem_actionPerformed(); + } + else if (source == font) + { + new FontChooser(alignPanel); + } else if (source == newView) + { newView(); - else if(source==showColumns) + } + else if (source == showColumns) { - viewport.showAllHiddenColumns(); alignPanel.repaint(); + viewport.showAllHiddenColumns(); + alignPanel.paintAlignment(true); } - else if(source==showSeqs) + else if (source == showSeqs) { viewport.showAllHiddenSeqs(); } - else if(source == hideColumns) + else if (source == hideColumns) { - viewport.hideSelectedColumns(); alignPanel.repaint(); + viewport.hideSelectedColumns(); + alignPanel.paintAlignment(true); } - else if(source == hideSequences && viewport.getSelectionGroup()!=null) + else if (source == hideSequences && viewport.getSelectionGroup() != null) { viewport.hideAllSelectedSeqs(); } - else if(source==featureSettings) - new FeatureSettings(alignPanel); - else if(source==overviewMenuItem) - overviewMenuItem_actionPerformed(); - else if(source==noColourmenuItem) - changeColour(null); - else if(source==clustalColour) + else if (source == featureSettings) + { + new FeatureSettings(alignPanel); + } + else if (source == overviewMenuItem) + { + overviewMenuItem_actionPerformed(); + } + else if (source == noColourmenuItem) + { + changeColour(null); + } + else if (source == clustalColour) { abovePIDThreshold.setState(false); changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth())); + } + else if (source == zappoColour) + { + changeColour(new ZappoColourScheme()); + } + else if (source == taylorColour) + { + changeColour(new TaylorColourScheme()); + } + else if (source == hydrophobicityColour) + { + changeColour(new HydrophobicColourScheme()); + } + else if (source == helixColour) + { + changeColour(new HelixColourScheme()); + } + else if (source == strandColour) + { + changeColour(new StrandColourScheme()); + } + else if (source == turnColour) + { + changeColour(new TurnColourScheme()); + } + else if (source == buriedColour) + { + changeColour(new BuriedColourScheme()); + } + else if (source == nucleotideColour) + { + changeColour(new NucleotideColourScheme()); + } + else if (source == modifyPID) + { + modifyPID_actionPerformed(); + } + else if (source == modifyConservation) + { + modifyConservation_actionPerformed(); + } + else if (source == userDefinedColour) + { + new UserDefinedColours(alignPanel, null); + } + else if (source == PIDColour) + { + changeColour(new PIDColourScheme()); + } + else if (source == BLOSUM62Colour) + { + changeColour(new Blosum62ColourScheme()); + } + else if (source == annotationColour) + { + new AnnotationColourChooser(viewport, alignPanel); + } + else if (source == sortPairwiseMenuItem) + { + sortPairwiseMenuItem_actionPerformed(); + } + else if (source == sortIDMenuItem) + { + sortIDMenuItem_actionPerformed(); + } + else if (source == sortGroupMenuItem) + { + sortGroupMenuItem_actionPerformed(); + } + else if (source == removeRedundancyMenuItem) + { + removeRedundancyMenuItem_actionPerformed(); + } + else if (source == pairwiseAlignmentMenuItem) + { + pairwiseAlignmentMenuItem_actionPerformed(); + } + else if (source == PCAMenuItem) + { + PCAMenuItem_actionPerformed(); + } + else if (source == averageDistanceTreeMenuItem) + { + averageDistanceTreeMenuItem_actionPerformed(); + } + else if (source == neighbourTreeMenuItem) + { + neighbourTreeMenuItem_actionPerformed(); + } + else if (source == njTreeBlosumMenuItem) + { + njTreeBlosumMenuItem_actionPerformed(); + } + else if (source == avDistanceTreeBlosumMenuItem) + { + avTreeBlosumMenuItem_actionPerformed(); + } + else if (source == documentation) + { + documentation_actionPerformed(); + } + else if (source == about) + { + about_actionPerformed(); + } + } - else if(source==zappoColour) - changeColour(new ZappoColourScheme()); - else if(source==taylorColour) - changeColour(new TaylorColourScheme()); - else if(source==hydrophobicityColour) - changeColour(new HydrophobicColourScheme()); - else if(source==helixColour) - changeColour(new HelixColourScheme()); - else if(source==strandColour) - changeColour(new StrandColourScheme()); - else if(source==turnColour) - changeColour(new TurnColourScheme()); - else if(source==buriedColour) - changeColour(new BuriedColourScheme()); - else if(source==nucleotideColour) - changeColour(new NucleotideColourScheme()); - else if(source==modifyPID) - modifyPID_actionPerformed(); - else if(source==modifyConservation) - modifyConservation_actionPerformed(); - else if(source==userDefinedColour) - new UserDefinedColours(alignPanel, null); - else if(source==PIDColour) - changeColour(new PIDColourScheme()); - else if(source==BLOSUM62Colour) - changeColour(new Blosum62ColourScheme()); - else if(source==annotationColour) - new AnnotationColourChooser(viewport, alignPanel); - else if(source==sortPairwiseMenuItem) - sortPairwiseMenuItem_actionPerformed(); - else if(source==sortIDMenuItem) - sortIDMenuItem_actionPerformed(); - else if(source==sortGroupMenuItem) - sortGroupMenuItem_actionPerformed(); - else if(source==removeRedundancyMenuItem) - removeRedundancyMenuItem_actionPerformed(); - else if(source==pairwiseAlignmentMenuItem) - pairwiseAlignmentMenuItem_actionPerformed(); - else if(source==PCAMenuItem) - PCAMenuItem_actionPerformed(); - else if(source==averageDistanceTreeMenuItem) - averageDistanceTreeMenuItem_actionPerformed(); - else if(source==neighbourTreeMenuItem) - neighbourTreeMenuItem_actionPerformed(); - else if(source==njTreeBlosumMenuItem) - njTreeBlosumMenuItem_actionPerformed(); - else if(source==avDistanceTreeBlosumMenuItem) - avTreeBlosumMenuItem_actionPerformed(); - else if(source==documentation) - documentation_actionPerformed(); - else if(source==about) - about_actionPerformed(); - - } public void inputText_actionPerformed() { @@ -648,75 +849,143 @@ public void itemStateChanged(ItemEvent evt) "Alignment output - " + e.getActionCommand(), 600, 500); cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), - viewport.getAlignment().getSequences(), - viewport.showJVSuffix)); + viewport.getAlignment(), + viewport.showJVSuffix)); + } + + public void loadAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your features / annotations file here."); + cap.setAnnotationImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300); + + } + + public String outputAnnotations(boolean displayTextbox) + { + String annotation = new AnnotationFile().printAnnotations( + viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null, + viewport.alignment.getGroups(), + ((Alignment)viewport.alignment).alignmentProperties); + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Annotations", + 600, 500); + cap.setText(annotation); + } + + return annotation; + } + + public String outputFeatures(boolean displayTextbox, String format) + { + String features; + if (format.equalsIgnoreCase("Jalview")) + { + features = new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + else + { + features = new FeaturesFile().printGFFFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed); + } + + if (displayTextbox) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Features", + 600, 500); + + cap.setText(features); + } + + return features; } void launchFullApplication() { StringBuffer url = new StringBuffer(jalviewServletURL); - url.append("?open="+ - appendProtocol( viewport.applet.getParameter("file") ) ); + url.append("?open=" + + appendProtocol(viewport.applet.getParameter("file"))); - if(viewport.applet.getParameter("features")!=null) + if (viewport.applet.getParameter("features") != null) { - url.append( "&features=" ); - url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + url.append("&features="); + url.append(appendProtocol(viewport.applet.getParameter("features"))); } - if(viewport.applet.getParameter("annotations")!=null) + if (viewport.applet.getParameter("annotations") != null) { - url.append( "&annotations=" ); - url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("annotations"))); } - if(viewport.applet.getParameter("jnetfile")!=null) + if (viewport.applet.getParameter("jnetfile") != null) { - url.append( "&annotations=" ); - url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) ); + url.append("&annotations="); + url.append(appendProtocol(viewport.applet.getParameter("jnetfile"))); } - if(viewport.applet.getParameter("defaultColour")!=null) + if (viewport.applet.getParameter("defaultColour") != null) { url.append("&colour=" + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) ); } - if(viewport.applet.getParameter("userDefinedColour")!=null) + if (viewport.applet.getParameter("userDefinedColour") != null) { - url.append( "&colour=" + - removeWhiteSpace( viewport.applet.getParameter("userDefinedColour") ) - ); + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter( + "userDefinedColour")) + ); } showURL(url.toString(), "FULL_APP"); } - String removeWhiteSpace(String colour) { StringBuffer sb = new StringBuffer(); for (int i = 0; i < colour.length(); i++) { if (Character.isWhitespace(colour.charAt(i))) + { sb.append("%20"); + } else + { sb.append(colour.charAt(i)); + } } return sb.toString(); } - String appendProtocol(String url) { - try{ - new URL(url); - }catch(java.net.MalformedURLException ex) + try + { + new URL(url); + } + catch (java.net.MalformedURLException ex) { - url = viewport.applet.getCodeBase()+url; + url = viewport.applet.getCodeBase() + url; } return url; } @@ -727,13 +996,14 @@ public void itemStateChanged(ItemEvent evt) PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); - if(PaintRefresher.components.size()==0 && viewport.applet==null) + if (PaintRefresher.components.size() == 0 && viewport.applet == null) + { System.exit(0); + } this.dispose(); } - /** * DOCUMENT ME! */ @@ -768,7 +1038,7 @@ public void itemStateChanged(ItemEvent evt) public void addHistoryItem(CommandI command) { - if(command.getSize()>0) + if (command.getSize() > 0) { viewport.historyList.push(command); viewport.redoList.removeAllElements(); @@ -784,10 +1054,12 @@ public void itemStateChanged(ItemEvent evt) */ protected void undoMenuItem_actionPerformed() { - if(viewport.historyList.size()<1) + if (viewport.historyList.size() < 1) + { return; + } - CommandI command = (CommandI)viewport.historyList.pop(); + CommandI command = (CommandI) viewport.historyList.pop(); viewport.redoList.push(command); command.undoCommand(); @@ -795,7 +1067,8 @@ public void itemStateChanged(ItemEvent evt) originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null,null); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } /** @@ -805,27 +1078,30 @@ public void itemStateChanged(ItemEvent evt) */ protected void redoMenuItem_actionPerformed() { - if(viewport.redoList.size()<1) + if (viewport.redoList.size() < 1) + { return; + } CommandI command = (CommandI) viewport.redoList.pop(); viewport.historyList.push(command); command.doCommand(); AlignViewport originalSource = getOriginatingSource(command); - originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns()!=null; + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; updateEditMenuBar(); - originalSource.firePropertyChange("alignment", null, null); + originalSource.firePropertyChange("alignment", null, + originalSource.alignment.getSequences()); } AlignViewport getOriginatingSource(CommandI command) { AlignViewport originalSource = null; //For sequence removal and addition, we need to fire - //the property change event FROM the viewport where the - //original alignment was altered - AlignmentI al = null; + //the property change event FROM the viewport where the + //original alignment was altered + AlignmentI al = null; if (command instanceof EditCommand) { EditCommand editCommand = (EditCommand) command; @@ -850,12 +1126,13 @@ public void itemStateChanged(ItemEvent evt) //The original view is closed, we must validate //the current view against the closed view first if (al != null) + { PaintRefresher.validateSequences(al, viewport.alignment); + } originalSource = viewport; } - return originalSource; } @@ -872,13 +1149,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(false).contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.getSequences(false).contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -892,13 +1169,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.getSequences(true).contains(seq)) + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.getSequences(true).contains(temp)) + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) { continue; } @@ -908,7 +1185,96 @@ public void itemStateChanged(ItemEvent evt) } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); + } + + synchronized void slideSequences(boolean right, int size) + { + Vector sg = new Vector(); + if(viewport.cursorMode) + { + sg.addElement(viewport.alignment.getSequenceAt( + alignPanel.seqPanel.seqCanvas.cursorY)); + } + else if(viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight()) + { + sg = viewport.getSelectionGroup().getSequences( + viewport.hiddenRepSequences); + } + + if(sg.size()<1) + { + return; + } + + Vector invertGroup = new Vector(); + + for (int i = 0; i < viewport.alignment.getHeight(); i++) + { + if(!sg.contains(viewport.alignment.getSequenceAt(i))) + invertGroup.addElement(viewport.alignment.getSequenceAt(i)); + } + + SequenceI[] seqs1 = new SequenceI[sg.size()]; + for (int i = 0; i < sg.size(); i++) + seqs1[i] = (SequenceI) sg.elementAt(i); + + SequenceI[] seqs2 = new SequenceI[invertGroup.size()]; + for (int i = 0; i < invertGroup.size(); i++) + seqs2[i] = (SequenceI) invertGroup.elementAt(i); + + SlideSequencesCommand ssc; + if (right) + ssc = new SlideSequencesCommand("Slide Sequences", + seqs2, seqs1, size, + viewport.getGapCharacter() + ); + else + ssc = new SlideSequencesCommand("Slide Sequences", + seqs1, seqs2, size, + viewport.getGapCharacter() + ); + + int groupAdjustment = 0; + if (ssc.getGapsInsertedBegin() && right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor(size, 0); + else + groupAdjustment = size; + } + else if (!ssc.getGapsInsertedBegin() && !right) + { + if (viewport.cursorMode) + alignPanel.seqPanel.moveCursor( -size, 0); + else + groupAdjustment = -size; + } + + if (groupAdjustment != 0) + { + viewport.getSelectionGroup().setStartRes( + viewport.getSelectionGroup().getStartRes() + groupAdjustment); + viewport.getSelectionGroup().setEndRes( + viewport.getSelectionGroup().getEndRes() + groupAdjustment); + } + + + boolean appendHistoryItem = false; + if(viewport.historyList!=null + && viewport.historyList.size()>0 + && viewport.historyList.peek() instanceof SlideSequencesCommand) + { + appendHistoryItem = ssc.appendSlideCommand( + (SlideSequencesCommand)viewport.historyList.peek()) + ; + } + + if(!appendHistoryItem) + addHistoryItem(ssc); + + repaint(); } static StringBuffer copiedSequences; @@ -923,7 +1289,7 @@ public void itemStateChanged(ItemEvent evt) SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -944,60 +1310,61 @@ public void itemStateChanged(ItemEvent evt) viewport.getColumnSelection().getHiddenColumns().elementAt(i); copiedHiddenColumns.addElement(new int[] - {region[0] - hiddenOffset, - region[1] - hiddenOffset}); + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); } } else + { copiedHiddenColumns = null; + } - - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { - SequenceI seq = null; + SequenceI seq = null; - while (seq == null) + while (seq == null) + { + if (orderedSeqs.containsKey(index + "")) { - if (orderedSeqs.containsKey(index + "")) - { - seq = (SequenceI) orderedSeqs.get(index + ""); - index++; + seq = (SequenceI) orderedSeqs.get(index + ""); + index++; - break; - } - else - { - index++; - } + break; } + else + { + index++; + } + } - //FIND START RES - //Returns residue following index if gap - startRes = seq.findPosition(sg.getStartRes()); + //FIND START RES + //Returns residue following index if gap + startRes = seq.findPosition(sg.getStartRes()); - //FIND END RES - //Need to find the residue preceeding index if gap - endRes = 0; + //FIND END RES + //Need to find the residue preceeding index if gap + endRes = 0; - for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++) + for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++) + { + ch = seq.getCharAt(j); + if (!jalview.util.Comparison.isGap( (ch))) { - ch = seq.getCharAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } + endRes++; } + } - if(endRes>0) - { - endRes += seq.getStart() -1; - } + if (endRes > 0) + { + endRes += seq.getStart() - 1; + } - copiedSequences.append(seq.getName() + "\t" + - startRes + "\t" + - endRes + "\t" + - seq.getSequence(sg.getStartRes(), - sg.getEndRes() + 1) + "\n"); + copiedSequences.append(seq.getName() + "\t" + + startRes + "\t" + + endRes + "\t" + + seq.getSequenceAsString(sg.getStartRes(), + sg.getEndRes() + 1) + "\n"); } } @@ -1061,30 +1428,12 @@ public void itemStateChanged(ItemEvent evt) } } - jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT); } else { - for (int i = 0; i < newSeqs.length; i++) - { - viewport.alignment.addSequence(newSeqs[i]); - } - - //!newAlignment - addHistoryItem(new EditCommand( - "Add sequences", - EditCommand.PASTE, - newSeqs, - 0, - viewport.alignment.getWidth(), - viewport.alignment) - ); - - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, null); + addSequences(newSeqs); } } @@ -1093,6 +1442,30 @@ public void itemStateChanged(ItemEvent evt) } + void addSequences(SequenceI[] seqs) + { + for (int i = 0; i < seqs.length; i++) + { + viewport.alignment.addSequence(seqs[i]); + } + + //!newAlignment + addHistoryItem(new EditCommand( + "Add sequences", + EditCommand.PASTE, + seqs, + 0, + viewport.alignment.getWidth(), + viewport.alignment) + ); + + viewport.setEndSeq(viewport.alignment.getHeight()); + viewport.alignment.getWidth(); + viewport.firePropertyChange("alignment", null, + viewport.alignment.getSequences()); + + } + protected void cut_actionPerformed() { copy_actionPerformed(); @@ -1110,56 +1483,54 @@ public void itemStateChanged(ItemEvent evt) Vector seqs = new Vector(); SequenceI seq; - for (int i = 0; i < sg.getSize(false); i++) + for (int i = 0; i < sg.getSize(); i++) { seq = sg.getSequenceAt(i); seqs.addElement(seq); } + // If the cut affects all sequences, remove highlighted columns + if (sg.getSize() == viewport.alignment.getHeight()) + { + viewport.getColumnSelection().removeElements(sg.getStartRes(), + sg.getEndRes() + 1); + } - // If the cut affects all sequences, remove highlighted columns - if (sg.getSize(false) == viewport.alignment.getHeight()) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } - - - SequenceI [] cut = new SequenceI[seqs.size()]; - for(int i=0; i 0) { - if(trimLeft) + if (trimLeft) + { column = colSel.getMin(); + } else + { column = colSel.getMax(); + } - SequenceI [] seqs; - if(viewport.getSelectionGroup()!=null) - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); + } else + { seqs = viewport.alignment.getSequencesArray(); - + } TrimRegionCommand trimRegion; - if(trimLeft) + if (trimLeft) { trimRegion = new TrimRegionCommand("Remove Left", - TrimRegionCommand.TRIM_LEFT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); + TrimRegionCommand.TRIM_LEFT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); viewport.setStartRes(0); } - else - { - trimRegion = new TrimRegionCommand("Remove Right", - TrimRegionCommand.TRIM_RIGHT, - seqs, - column, - viewport.alignment, - viewport.colSel, - viewport.selectionGroup); - } - - statusBar.setText("Removed "+trimRegion.getSize()+" columns."); + else + { + trimRegion = new TrimRegionCommand("Remove Right", + TrimRegionCommand.TRIM_RIGHT, + seqs, + column, + viewport.alignment, + viewport.colSel, + viewport.selectionGroup); + } + statusBar.setText("Removed " + trimRegion.getSize() + " columns."); addHistoryItem(trimRegion); @@ -1267,59 +1645,64 @@ public void itemStateChanged(ItemEvent evt) } } - public void removeGappedColumnMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.alignment.getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else + { seqs = viewport.alignment.getSequencesArray(); - + } RemoveGapColCommand removeGapCols = new RemoveGapColCommand("Remove Gapped Columns", seqs, start, end, - viewport.getGapCharacter()); + viewport.alignment); addHistoryItem(removeGapCols); - statusBar.setText("Removed "+removeGapCols.getSize()+" empty columns."); + statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns."); //This is to maintain viewport position on first residue //of first sequence SequenceI seq = viewport.alignment.getSequenceAt(0); int startRes = seq.findPosition(viewport.startRes); - // ShiftList shifts; - // viewport.getAlignment().removeGaps(shifts=new ShiftList()); - // edit.alColumnChanges=shifts.getInverse(); - // if (viewport.hasHiddenColumns) - // viewport.getColumnSelection().compensateForEdits(shifts); - viewport.setStartRes(seq.findIndex(startRes)-1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + // ShiftList shifts; + // viewport.getAlignment().removeGaps(shifts=new ShiftList()); + // edit.alColumnChanges=shifts.getInverse(); + // if (viewport.hasHiddenColumns) + // viewport.getColumnSelection().compensateForEdits(shifts); + viewport.setStartRes(seq.findIndex(startRes) - 1); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } public void removeAllGapsMenuItem_actionPerformed() { - int start = 0, end = viewport.alignment.getWidth()-1; + int start = 0, end = viewport.alignment.getWidth() - 1; SequenceI[] seqs; if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().getSequencesAsArray(true); + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport. + hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes(); } else + { seqs = viewport.alignment.getSequencesArray(); + } //This is to maintain viewport position on first residue //of first sequence @@ -1327,13 +1710,14 @@ public void itemStateChanged(ItemEvent evt) int startRes = seq.findPosition(viewport.startRes); addHistoryItem(new RemoveGapsCommand("Remove Gaps", - seqs, - start, end, - viewport.getGapCharacter())); + seqs, + start, end, + viewport.alignment)); - viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.setStartRes(seq.findIndex(startRes) - 1); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); } @@ -1346,12 +1730,27 @@ public void itemStateChanged(ItemEvent evt) { AlignmentI newal; if (viewport.hasHiddenRows) + { newal = new Alignment(viewport.getAlignment(). getHiddenSequences() .getFullAlignment(). getSequencesArray()); + } else + { newal = new Alignment(viewport.alignment.getSequencesArray()); + } + + if (viewport.alignment.getAlignmentAnnotation() != null) + { + for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++) + { + if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated) + { + newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]); + } + } + } AlignFrame newaf = new AlignFrame(newal, viewport.applet, @@ -1368,41 +1767,43 @@ public void itemStateChanged(ItemEvent evt) PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, newaf.alignPanel.av.getSequenceSetId()); - Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId()); + Vector comps = (Vector) PaintRefresher.components.get(viewport. + getSequenceSetId()); int viewSize = -1; for (int i = 0; i < comps.size(); i++) { if (comps.elementAt(i) instanceof AlignmentPanel) + { viewSize++; + } } String title = new String(this.getTitle()); if (title.indexOf("(View") > -1) + { title = title.substring(0, title.indexOf("(View")); + } - title+= "(View "+viewSize+")"; + title += "(View " + viewSize + ")"; newaf.setTitle(title.toString()); - newaf.viewport.historyList = viewport.historyList; newaf.viewport.redoList = viewport.redoList; - } - + } public void seqLimits_itemStateChanged() { viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } protected void wrapMenuItem_actionPerformed() @@ -1412,10 +1813,9 @@ public void itemStateChanged(ItemEvent evt) scaleAbove.setEnabled(wrapMenuItem.getState()); scaleLeft.setEnabled(wrapMenuItem.getState()); scaleRight.setEnabled(wrapMenuItem.getState()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } - public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) @@ -1428,8 +1828,8 @@ public void itemStateChanged(ItemEvent evt) frame.add(overview); // +50 must allow for applet frame window jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(), - overview.preferredSize().width, - overview.preferredSize().height + 50); + overview.getPreferredSize().width, + overview.getPreferredSize().height + 50); frame.pack(); frame.addWindowListener(new WindowAdapter() @@ -1444,12 +1844,11 @@ public void itemStateChanged(ItemEvent evt) } - void changeColour(ColourSchemeI cs) { int threshold = 0; - if(cs!=null) + if (cs != null) { if (viewport.getAbovePIDThreshold()) { @@ -1499,14 +1898,16 @@ public void itemStateChanged(ItemEvent evt) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if(cs==null) + if (cs == null) { sg.cs = null; continue; } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else { @@ -1526,16 +1927,20 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); } else + { sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); + } if (viewport.getConservationSelected()) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.getSequences(true), 0, + sg.getSequences(viewport. + hiddenRepSequences), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1550,20 +1955,20 @@ public void itemStateChanged(ItemEvent evt) } } - if (alignPanel.getOverviewPanel() != null) { alignPanel.getOverviewPanel().updateOverviewImage(); } - alignPanel.repaint(); - } - + jalview.structure.StructureSelectionManager.getStructureSelectionManager() + .sequenceColoursChanged(alignPanel); + alignPanel.paintAlignment(true); + } protected void modifyPID_actionPerformed() { - if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) + if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null) { SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(), "Background"); @@ -1573,7 +1978,7 @@ public void itemStateChanged(ItemEvent evt) protected void modifyConservation_actionPerformed() { - if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) + if (viewport.getConservationSelected() && viewport.globalColourScheme != null) { SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme, "Background"); @@ -1605,43 +2010,42 @@ public void itemStateChanged(ItemEvent evt) modifyPID_actionPerformed(); } - - public void sortPairwiseMenuItem_actionPerformed() { - SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); + SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); - addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment)); - alignPanel.repaint(); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, + viewport.alignment)); + alignPanel.paintAlignment(true); } public void sortIDMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, - // HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByID(viewport.getAlignment()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void sortGroupMenuItem_actionPerformed() { - // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, - // HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByGroup(viewport.getAlignment()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } public void removeRedundancyMenuItem_actionPerformed() { - new RedundancyPanel(alignPanel); + new RedundancyPanel(alignPanel); } public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup()!=null - && viewport.getSelectionGroup().getSize(false) > 1) + if (viewport.getSelectionGroup() != null + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1667,12 +2071,12 @@ public void itemStateChanged(ItemEvent evt) current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) < 4 && - viewport.getSelectionGroup().getSize(false) > 0) + viewport.getSelectionGroup().getSize() < 4 && + viewport.getSelectionGroup().getSize() > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1705,7 +2109,7 @@ public void itemStateChanged(ItemEvent evt) protected void avTreeBlosumMenuItem_actionPerformed() { - NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); + NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62"); } void NewTreePanel(String type, String pwType, String title) @@ -1726,14 +2130,14 @@ public void itemStateChanged(ItemEvent evt) current.insertCharAt(Width - 1, viewport.getGapCharacter()); } } - alignPanel.repaint(); + alignPanel.paintAlignment(true); } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize(false) > 1) - || (viewport.getSelectionGroup() == null - && viewport.alignment.getHeight() > 1)) + viewport.getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) { final TreePanel tp = new TreePanel(viewport, type, @@ -1747,12 +2151,12 @@ public void itemStateChanged(ItemEvent evt) void loadTree_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); - cap.setText("Paste your Newick tree file here."); - cap.setTreeImport(); - Frame frame = new Frame(); - frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); + cap.setText("Paste your Newick tree file here."); + cap.setTreeImport(); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300); } public void loadTree(jalview.io.NewickFile tree, String treeFile) @@ -1773,10 +2177,10 @@ public void itemStateChanged(ItemEvent evt) { public void actionPerformed(ActionEvent evt) { - // addHistoryItem(new HistoryItem("Sort", viewport.alignment, - // HistoryItem.SORT)); + // addHistoryItem(new HistoryItem("Sort", viewport.alignment, + // HistoryItem.SORT)); AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree()); - alignPanel.repaint(); + alignPanel.paintAlignment(true); } }); @@ -1797,11 +2201,14 @@ public void itemStateChanged(ItemEvent evt) protected void about_actionPerformed() { - class AboutPanel extends Canvas + class AboutPanel + extends Canvas { String version; public AboutPanel(String version) - { this.version = version; } + { + this.version = version; + } public void paint(Graphics g) { @@ -1813,7 +2220,7 @@ public void itemStateChanged(ItemEvent evt) int y = 5, x = 7; g.setColor(Color.black); g.setFont(new Font("Helvetica", Font.BOLD, 14)); - g.drawString("Jalview - Release "+version, 200, y += fh); + g.drawString("Jalview - Release " + version, 200, y += fh); g.setFont(new Font("Helvetica", Font.PLAIN, 12)); g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.", x, y += fh * 2); @@ -1852,7 +2259,6 @@ public void itemStateChanged(ItemEvent evt) } } - Frame frame = new Frame(); frame.add(new AboutPanel(version)); jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); @@ -1869,9 +2275,9 @@ public void itemStateChanged(ItemEvent evt) { try { - System.out.println("Show url: "+url); + System.out.println("Show url: " + url); viewport.applet.getAppletContext().showDocument(new java.net.URL(url), - target); + target); } catch (Exception ex) { @@ -1880,88 +2286,92 @@ public void itemStateChanged(ItemEvent evt) } } - ////////////////////////////////////////////////////////////////////////////////// //JBuilder Graphics here - protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu("File"); - protected MenuItem loadApplication = new MenuItem("View in Full Application"); - protected MenuItem loadTree = new MenuItem("Load Associated Tree"); - protected MenuItem closeMenuItem = new MenuItem("Close"); - protected Menu editMenu = new Menu("Edit"); - protected Menu viewMenu = new Menu("View"); - protected Menu colourMenu = new Menu("Colour"); - protected Menu calculateMenu = new Menu("Calculate"); - protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); - protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); - protected MenuItem remove2LeftMenuItem = new MenuItem(); - protected MenuItem remove2RightMenuItem = new MenuItem(); - protected MenuItem removeGappedColumnMenuItem = new MenuItem(); - protected MenuItem removeAllGapsMenuItem = new MenuItem(); - protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); - protected MenuItem sortPairwiseMenuItem = new MenuItem(); - protected MenuItem sortIDMenuItem = new MenuItem(); - protected MenuItem sortGroupMenuItem = new MenuItem(); - protected MenuItem removeRedundancyMenuItem = new MenuItem(); - protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); - protected MenuItem PCAMenuItem = new MenuItem(); - protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); - protected MenuItem neighbourTreeMenuItem = new MenuItem(); - BorderLayout borderLayout1 = new BorderLayout(); - public Label statusBar = new Label(); - protected Menu outputTextboxMenu = new Menu(); - protected MenuItem clustalColour = new MenuItem(); - protected MenuItem zappoColour = new MenuItem(); - protected MenuItem taylorColour = new MenuItem(); - protected MenuItem hydrophobicityColour = new MenuItem(); - protected MenuItem helixColour = new MenuItem(); - protected MenuItem strandColour = new MenuItem(); - protected MenuItem turnColour = new MenuItem(); - protected MenuItem buriedColour = new MenuItem(); - protected MenuItem userDefinedColour = new MenuItem(); - protected MenuItem PIDColour = new MenuItem(); - protected MenuItem BLOSUM62Colour = new MenuItem(); - MenuItem njTreeBlosumMenuItem = new MenuItem(); - MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); - protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); - MenuItem overviewMenuItem = new MenuItem(); - protected MenuItem undoMenuItem = new MenuItem(); - protected MenuItem redoMenuItem = new MenuItem(); - protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); - MenuItem noColourmenuItem = new MenuItem(); - protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); - protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); - MenuItem findMenuItem = new MenuItem(); + protected MenuBar alignFrameMenuBar = new MenuBar(); + protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); + protected MenuItem loadTree = new MenuItem("Load Associated Tree ..."); + protected MenuItem loadAnnotations = new MenuItem( + "Load Features/Annotations ..."); + protected MenuItem outputFeatures = new MenuItem("Export Features ..."); + protected MenuItem outputAnnotations = new MenuItem("Export Annotations ..."); + + protected MenuItem closeMenuItem = new MenuItem("Close"); + protected Menu editMenu = new Menu("Edit"); + protected Menu viewMenu = new Menu("View"); + protected Menu colourMenu = new Menu("Colour"); + protected Menu calculateMenu = new Menu("Calculate"); + protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all"); + protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All"); + protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection"); + protected MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); - protected MenuItem nucleotideColour = new MenuItem(); - MenuItem deleteGroups = new MenuItem(); - MenuItem delete = new MenuItem(); - MenuItem copy = new MenuItem(); - MenuItem cut = new MenuItem(); - Menu pasteMenu = new Menu(); - MenuItem pasteNew = new MenuItem(); - MenuItem pasteThis = new MenuItem(); - protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); - protected MenuItem font = new MenuItem(); - protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); - protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); - MenuItem modifyPID = new MenuItem(); - MenuItem modifyConservation = new MenuItem(); - protected CheckboxMenuItem autoCalculate - = new CheckboxMenuItem("Autocalculate Consensus", true); - protected Menu sortByTreeMenu = new Menu(); - Menu sort = new Menu(); - Menu calculate = new Menu(); - MenuItem inputText = new MenuItem(); - Menu helpMenu = new Menu(); - MenuItem documentation = new MenuItem(); - MenuItem about = new MenuItem(); - protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); Panel embeddedMenu; Label embeddedEdit; Label embeddedSelect; @@ -1973,174 +2383,179 @@ public void itemStateChanged(ItemEvent evt) Label embeddedCalculate; FlowLayout flowLayout1; - private void jbInit() throws Exception { + private void jbInit() + throws Exception + { - setMenuBar(alignFrameMenuBar); + setMenuBar(alignFrameMenuBar); - MenuItem item; + MenuItem item; - // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) - { + // dynamically fill save as menu with available formats + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; + i++) + { - item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); - item.addActionListener(new java.awt.event.ActionListener() + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) { - public void actionPerformed(ActionEvent e) - { - outputText_actionPerformed(e); - } - }); - - outputTextboxMenu.add(item); - } - closeMenuItem.addActionListener(this); - loadApplication.addActionListener(this); - - loadTree.addActionListener(this); - selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.addActionListener(this); - remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(this); - remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(this); - removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(this); - removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(this); - viewBoxesMenuItem.setLabel("Boxes"); - viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(this); - viewTextMenuItem.setLabel("Text"); - viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(this); - sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(this); - sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(this); - sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(this); - removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(this); - pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(this); - PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(this); - averageDistanceTreeMenuItem.setLabel( - "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(this); - neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(this); - alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setBackground(Color.white); - statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); - statusBar.setText("Status bar"); - outputTextboxMenu.setLabel("Output to Textbox"); - clustalColour.setLabel("Clustalx"); - - clustalColour.addActionListener(this); - zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(this); - taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(this); - hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(this); - helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(this); - strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(this); - turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(this); - buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(this); - userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(this); - PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(this); - BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(this); - avDistanceTreeBlosumMenuItem.setLabel( - "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(this); - njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(this); - annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(this); - colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(this); - overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(this); - undoMenuItem.setEnabled(false); - undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(this); - redoMenuItem.setEnabled(false); - redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(this); - conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(this); - noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(this); - wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(this); - renderGapsMenuItem.setLabel("Show Gaps"); - renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(this); - findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(this); + outputText_actionPerformed(e); + } + }); + + outputTextboxMenu.add(item); + } + closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); + + loadTree.addActionListener(this); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(this); - nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(this); - deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(this); - copy.setLabel("Copy"); - copy.addActionListener(this); - cut.setLabel("Cut"); - cut.addActionListener(this); - delete.setLabel("Delete"); - delete.addActionListener(this); - pasteMenu.setLabel("Paste"); - pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(this); - pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(this); - applyToAllGroups.setLabel("Apply Colour To All Groups"); - applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(this); - font.setLabel("Font..."); - font.addActionListener(this); - scaleAbove.setLabel("Scale Above"); - scaleAbove.setState(true); - scaleAbove.setEnabled(false); - scaleAbove.addItemListener(this); - scaleLeft.setEnabled(false); - scaleLeft.setState(true); - scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(this); - scaleRight.setEnabled(false); - scaleRight.setState(true); - scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(this); - modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(this); - modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(this); - sortByTreeMenu.setLabel("By Tree Order"); - sort.setLabel("Sort"); - calculate.setLabel("Calculate Tree"); - autoCalculate.addItemListener(this); - inputText.setLabel("Input from textbox"); - inputText.addActionListener(this); - - helpMenu.setLabel("Help"); - documentation.setLabel("Documentation"); - documentation.addActionListener(this); - - about.setLabel("About..."); - about.addActionListener(this); - seqLimits.setState(true); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); seqLimits.setLabel("Show Sequence Limits"); seqLimits.addItemListener(this); featureSettings.setLabel("Feature Settings..."); @@ -2168,32 +2583,43 @@ public void itemStateChanged(ItemEvent evt) newView.setLabel("New View"); newView.addActionListener(this); alignFrameMenuBar.add(fileMenu); - alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(editMenu); alignFrameMenuBar.add(selectMenu); alignFrameMenuBar.add(viewMenu); alignFrameMenuBar.add(formatMenu); alignFrameMenuBar.add(colourMenu); - alignFrameMenuBar.add(calculateMenu); - alignFrameMenuBar.add(helpMenu); - fileMenu.add(inputText); - fileMenu.add(outputTextboxMenu); - if(jalviewServletURL!=null) - fileMenu.add(loadApplication); - fileMenu.addSeparator(); - fileMenu.add(loadTree); - fileMenu.add(closeMenuItem); - editMenu.add(undoMenuItem); - editMenu.add(redoMenuItem); - editMenu.add(cut); - editMenu.add(copy); - editMenu.add(pasteMenu); - editMenu.add(delete); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + + fileMenu.add(inputText); + fileMenu.add(loadTree); + fileMenu.add(loadAnnotations); + + fileMenu.addSeparator(); + fileMenu.add(outputTextboxMenu); + fileMenu.add(outputFeatures); + fileMenu.add(outputAnnotations); + + if (jalviewServletURL != null) + { + fileMenu.add(loadApplication); + } + + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); editMenu.addSeparator(); - editMenu.add(remove2LeftMenuItem); - editMenu.add(remove2RightMenuItem); - editMenu.add(removeGappedColumnMenuItem); - editMenu.add(removeAllGapsMenuItem); - editMenu.add(removeRedundancyMenuItem); + editMenu.add(remove2LeftMenuItem); + editMenu.add(remove2RightMenuItem); + editMenu.add(removeGappedColumnMenuItem); + editMenu.add(removeAllGapsMenuItem); + editMenu.add(removeRedundancyMenuItem); viewMenu.add(newView); viewMenu.addSeparator(); viewMenu.add(menu1); @@ -2201,50 +2627,50 @@ public void itemStateChanged(ItemEvent evt) viewMenu.addSeparator(); viewMenu.add(annotationPanelMenuItem); viewMenu.addSeparator(); - viewMenu.add(sequenceFeatures); - viewMenu.add(featureSettings); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); - viewMenu.add(overviewMenuItem); - colourMenu.add(applyToAllGroups); - colourMenu.addSeparator(); - colourMenu.add(noColourmenuItem); - colourMenu.add(clustalColour); - colourMenu.add(BLOSUM62Colour); - colourMenu.add(PIDColour); - colourMenu.add(zappoColour); - colourMenu.add(taylorColour); - colourMenu.add(hydrophobicityColour); - colourMenu.add(helixColour); - colourMenu.add(strandColour); - colourMenu.add(turnColour); - colourMenu.add(buriedColour); - colourMenu.add(nucleotideColour); - colourMenu.add(userDefinedColour); - colourMenu.addSeparator(); - colourMenu.add(conservationMenuItem); - colourMenu.add(modifyConservation); - colourMenu.add(abovePIDThreshold); - colourMenu.add(modifyPID); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); colourMenu.add(annotationColour); calculateMenu.add(sort); - calculateMenu.add(calculate); - calculateMenu.addSeparator(); - calculateMenu.add(pairwiseAlignmentMenuItem); - calculateMenu.add(PCAMenuItem); - calculateMenu.add(autoCalculate); - this.add(statusBar, BorderLayout.SOUTH); - pasteMenu.add(pasteNew); - pasteMenu.add(pasteThis); - sort.add(sortIDMenuItem); - sort.add(sortByTreeMenu); - sort.add(sortGroupMenuItem); - sort.add(sortPairwiseMenuItem); - calculate.add(averageDistanceTreeMenuItem); - calculate.add(neighbourTreeMenuItem); - calculate.add(avDistanceTreeBlosumMenuItem); - calculate.add(njTreeBlosumMenuItem); - helpMenu.add(documentation); - helpMenu.add(about); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); menu1.add(showColumns); menu1.add(showSeqs); menu2.add(hideColumns); @@ -2311,27 +2737,24 @@ public void itemStateChanged(ItemEvent evt) embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); - // setVisible(false); fileMenu.remove(closeMenuItem); fileMenu.remove(3); // Seperator viewport.applet.setLayout(new BorderLayout()); viewport.applet.add(embeddedMenu, BorderLayout.NORTH); viewport.applet.add(statusBar, BorderLayout.SOUTH); - // viewport.applet.validate(); - alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height + alignPanel.setSize(viewport.applet.getSize().width, + viewport.applet.getSize().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); - viewport.applet.add(alignPanel, BorderLayout.CENTER); - viewport.applet.validate(); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); } - - PopupMenu filePopup, editPopup, searchPopup, - viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; + viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); MenuItem annotationColour = new MenuItem(); @@ -2349,36 +2772,36 @@ public void itemStateChanged(ItemEvent evt) public void mousePressed(MouseEvent evt) { PopupMenu popup = null; - Label source = (Label)evt.getSource(); - if(source==embeddedFile) + Label source = (Label) evt.getSource(); + if (source == embeddedFile) { popup = filePopup = genPopupMenu(filePopup, fileMenu); } - else if(source==embeddedEdit) + else if (source == embeddedEdit) { popup = editPopup = genPopupMenu(editPopup, editMenu); } - else if(source==embeddedSelect) + else if (source == embeddedSelect) { popup = searchPopup = genPopupMenu(searchPopup, selectMenu); } - else if(source==embeddedView) + else if (source == embeddedView) { popup = viewPopup = genPopupMenu(viewPopup, viewMenu); } - else if (source ==embeddedFormat) + else if (source == embeddedFormat) { popup = formatPopup = genPopupMenu(formatPopup, formatMenu); } - else if(source==embeddedColour) + else if (source == embeddedColour) { popup = colourPopup = genPopupMenu(colourPopup, colourMenu); } - else if(source==embeddedCalculate) + else if (source == embeddedCalculate) { popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); } - else if(source==embeddedHelp) + else if (source == embeddedHelp) { popup = helpPopup = genPopupMenu(helpPopup, helpMenu); } @@ -2391,13 +2814,13 @@ public void itemStateChanged(ItemEvent evt) PopupMenu genPopupMenu(PopupMenu popup, Menu original) { - if(popup!=null) + if (popup != null) { return popup; } popup = new PopupMenu(); int m, mSize = original.getItemCount(); - for(m=0; m