X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=147e035ff6ea6bfa293f607472d1b2ac7b919cb4;hb=0452450533728e478ef8c893ea2cb3483c740fb3;hp=fbe21b58de07ce093470a56454e5cfa6093c2bde;hpb=1d37661bae76ec6d499ff50a88ea249b8b33430e;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index fbe21b5..147e035 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) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Copyright (C) 2006 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 @@ -23,6 +23,7 @@ import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; import jalview.io.*; +import jalview.commands.*; import java.awt.*; import java.awt.event.*; import java.util.*; @@ -36,13 +37,21 @@ public class AlignFrame extends Frame implements ActionListener, { public AlignmentPanel alignPanel; public AlignViewport viewport; - int NEW_WINDOW_WIDTH = 700; - int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + int DEFAULT_WIDTH = 700; + int DEFAULT_HEIGHT = 500; + String jalviewServletURL; - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) + + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) { + + if (applet != null) + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + try{ jbInit(); }catch(Exception ex) @@ -50,12 +59,16 @@ public class AlignFrame extends Frame implements ActionListener, ex.printStackTrace(); } - this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); + viewport.updateConservation(alignPanel); + viewport.updateConsensus(alignPanel); + annotationPanelMenuItem.setState(viewport.showAnnotation); + seqLimits.setState(viewport.showJVSuffix); + if(applet!=null) { String param = applet.getParameter("sortBy"); @@ -83,13 +96,13 @@ public class AlignFrame extends Frame implements ActionListener, if (param != null) { int width = Integer.parseInt(param); - NEW_WINDOW_WIDTH = width; + DEFAULT_WIDTH = width; } param = applet.getParameter("windowHeight"); if (param != null) { int height = Integer.parseInt(param); - NEW_WINDOW_HEIGHT = height; + DEFAULT_HEIGHT = height; } } catch (Exception ex) @@ -102,22 +115,20 @@ public class AlignFrame extends Frame implements ActionListener, this.addKeyListener(this); alignPanel.seqPanel.seqCanvas.addKeyListener(this); alignPanel.idPanel.idCanvas.addKeyListener(this); - - viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() - { - public void propertyChange(java.beans.PropertyChangeEvent evt) - { - if (evt.getPropertyName().equals("alignment")) - { - alignmentChanged(); - } - } - }); - - - add(alignPanel, BorderLayout.CENTER); - jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); - + 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(); } @@ -138,87 +149,44 @@ public class AlignFrame extends Frame implements ActionListener, * @param String DOCUMENT ME! */ - public void parseFeaturesFile(String file) + public void parseFeaturesFile(String file, String type) { - try + 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); + } + catch(Exception ex) { - URL url = new URL(file); - - BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); - SequenceI seq = null; - String line, type, desc, token; - - int index, start, end; - StringTokenizer st; - SequenceFeature sf; - FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - int lineNo = 0; - while ( (line = in.readLine()) != null) - { - lineNo++; - st = new StringTokenizer(line, "\t"); - if (st.countTokens() == 2) - { - type = st.nextToken(); - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - fr.setColour(type, ucs.findColour("A")); - continue; - } - - while (st.hasMoreElements()) - { - desc = st.nextToken(); - token = st.nextToken(); - if (!token.equals("ID_NOT_SPECIFIED")) - { - index = viewport.alignment.findIndex(viewport.alignment.findName( - token)); - st.nextToken(); - } - else - { - index = Integer.parseInt(st.nextToken()); - } - - start = Integer.parseInt(st.nextToken()); - end = Integer.parseInt(st.nextToken()); - - seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start) - 1; - end = seq.findIndex(end) - 1; - - type = st.nextToken(); - - if(fr.getColour(type)==null) - { - // Probably the old style groups file - UserColourScheme ucs = new UserColourScheme(type); - fr.setColour(type, ucs.findColour("A")); - } - - sf = new SequenceFeature(type, desc, "", start, end); - - seq.addSequenceFeature(sf); - } - } + ex.printStackTrace(); + } + if(featuresFile) + { + if(featureLinks.size()>0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; viewport.showSequenceFeatures = true; - viewMenu.addSeparator(); - viewMenu.add(sequenceFeatures); - viewMenu.add(featureSettings); - - + sequenceFeatures.setState(true); alignPanel.repaint(); - - } - catch (Exception ex) - { - System.out.println("Error parsing groups file: " + ex); } + } + public void keyPressed(KeyEvent evt) { + if (viewport.cursorMode + && evt.getKeyCode() >= KeyEvent.VK_0 + && evt.getKeyCode() <= KeyEvent.VK_9) + { + alignPanel.seqPanel.numberPressed(evt.getKeyChar()); + } + switch (evt.getKeyCode()) { case 27: // escape key @@ -231,15 +199,19 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } if (evt.isControlDown() || evt.isMetaDown()) { copy_actionPerformed(); } break; case KeyEvent.VK_V: - if (evt.isControlDown() || evt.isMetaDown()) + if (evt.isControlDown()) { - paste(true); + paste(evt.isShiftDown()); } break; case KeyEvent.VK_A: @@ -249,22 +221,227 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - moveSelectedSequences(false); + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); break; + case KeyEvent.VK_UP: - moveSelectedSequences(true); + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,-1); + } + else + moveSelectedSequences(true); + break; + + case KeyEvent.VK_LEFT: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(1,0); + } + break; + case KeyEvent.VK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown() + ); + } break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown() + || evt.isShiftDown() + || evt.isAltDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + 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_F: if (evt.isControlDown()) { findMenuItem_actionPerformed(); } break; - case KeyEvent.VK_BACK_SPACE: - case KeyEvent.VK_DELETE: - cut_actionPerformed(); + + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); + + if(toggleSeqs) + { + if (sg != null && sg.getSize() != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + viewport.showAllHiddenSeqs(); + } + + if(toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + 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: + if (evt.isControlDown()) + { + undoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_Y: + if (evt.isControlDown()) + { + redoMenuItem_actionPerformed(); + } + break; + + case KeyEvent.VK_L: + if (evt.isControlDown()) + { + trimAlignment(true); + } + break; + + case KeyEvent.VK_R: + if (evt.isControlDown()) + { + trimAlignment(false); + } + break; + + case KeyEvent.VK_E: + 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; + + case KeyEvent.VK_U: + if (evt.isControlDown()) + { + this.deleteGroups_actionPerformed(); + } + break; + + case KeyEvent.VK_T: + if (evt.isControlDown()) + { + newView(); + } + break; + + + } + alignPanel.repaint(); } public void keyReleased(KeyEvent evt) {} @@ -278,146 +455,192 @@ public void itemStateChanged(ItemEvent evt) else if(evt.getSource()==wrapMenuItem) wrapMenuItem_actionPerformed(); else if(evt.getSource()==scaleAbove) - scaleAbove_actionPerformed(); + viewport.setScaleAboveWrapped(scaleAbove.getState()); else if(evt.getSource()==scaleLeft) - scaleLeft_actionPerformed(); + viewport.setScaleLeftWrapped(scaleLeft.getState()); else if(evt.getSource()==scaleRight) - scaleRight_actionPerformed(); + viewport.setScaleRightWrapped(scaleRight.getState()); else if(evt.getSource()==seqLimits) seqLimits_itemStateChanged(); else if(evt.getSource()==viewBoxesMenuItem) - viewBoxesMenuItem_actionPerformed(); + viewport.setShowBoxes(viewBoxesMenuItem.getState()); else if(evt.getSource()==viewTextMenuItem) - viewTextMenuItem_actionPerformed(); + viewport.setShowText(viewTextMenuItem.getState()); else if(evt.getSource()==renderGapsMenuItem) - renderGapsMenuItem_actionPerformed(); + viewport.setRenderGaps(renderGapsMenuItem.getState()); else if(evt.getSource()==annotationPanelMenuItem) - annotationPanelMenuItem_actionPerformed(); + { + viewport.setShowAnnotation(annotationPanelMenuItem.getState()); + alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); + } else if(evt.getSource()==sequenceFeatures) - { viewport.showSequenceFeatures(sequenceFeatures.getState()); + { + 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) - applyToAllGroups_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) { - if(evt.getSource()==inputText) + Object source = evt.getSource(); + + if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==closeMenuItem) + else if(source==loadTree) + loadTree_actionPerformed(); + else if(source==loadApplication) + launchFullApplication(); + else if (source == loadAnnotations) + loadAnnotations(); + else if (source == outputAnnotations) + outputAnnotations(); + else if(source == outputFeatures) + outputFeatures(); + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==inputText) + else if(source==inputText) inputText_actionPerformed(); - else if(evt.getSource()==closeMenuItem) + else if(source==closeMenuItem) closeMenuItem_actionPerformed(); - else if(evt.getSource()==undoMenuItem) + else if(source==undoMenuItem) undoMenuItem_actionPerformed(); - else if(evt.getSource()==redoMenuItem) + else if(source==redoMenuItem) redoMenuItem_actionPerformed(); - else if(evt.getSource()==copy) + else if(source==copy) copy_actionPerformed(); - else if(evt.getSource()==pasteNew) + else if(source==pasteNew) pasteNew_actionPerformed(); - else if(evt.getSource()==pasteThis) + else if(source==pasteThis) pasteThis_actionPerformed(); - else if(evt.getSource()==cut) + else if(source==cut) cut_actionPerformed(); - else if(evt.getSource()==delete) + else if(source==delete) delete_actionPerformed(); - else if(evt.getSource()==deleteGroups) + else if(source==deleteGroups) deleteGroups_actionPerformed(); - else if(evt.getSource()==selectAllSequenceMenuItem) + else if(source==selectAllSequenceMenuItem) selectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==deselectAllSequenceMenuItem) + else if(source==deselectAllSequenceMenuItem) deselectAllSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==invertSequenceMenuItem) + else if(source==invertSequenceMenuItem) invertSequenceMenuItem_actionPerformed(); - else if(evt.getSource()==remove2LeftMenuItem) - remove2LeftMenuItem_actionPerformed(); - else if(evt.getSource()==remove2RightMenuItem) - remove2RightMenuItem_actionPerformed(); - else if(evt.getSource()==removeGappedColumnMenuItem) + 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(evt.getSource()==removeAllGapsMenuItem) + else if(source==removeAllGapsMenuItem) removeAllGapsMenuItem_actionPerformed(); - else if(evt.getSource()==findMenuItem) + else if(source==findMenuItem) findMenuItem_actionPerformed(); - else if(evt.getSource()==font) - font_actionPerformed(); - else if(evt.getSource()==featureSettings) - featureSettings_actionPerformed(); - else if(evt.getSource()==overviewMenuItem) + else if(source==font) + new FontChooser(alignPanel); + else if (source == newView) + newView(); + else if(source==showColumns) + { + viewport.showAllHiddenColumns(); alignPanel.repaint(); + } + else if(source==showSeqs) + { + viewport.showAllHiddenSeqs(); + } + else if(source == hideColumns) + { + viewport.hideSelectedColumns(); alignPanel.repaint(); + } + else if(source == hideSequences && viewport.getSelectionGroup()!=null) + { + viewport.hideAllSelectedSeqs(); + } + else if(source==featureSettings) + new FeatureSettings(alignPanel); + else if(source==overviewMenuItem) overviewMenuItem_actionPerformed(); - else if(evt.getSource()==noColourmenuItem) - noColourmenuItem_actionPerformed(); - else if(evt.getSource()==clustalColour) - clustalColour_actionPerformed(); - else if(evt.getSource()==zappoColour) - zappoColour_actionPerformed(); - else if(evt.getSource()==taylorColour) - taylorColour_actionPerformed(); - else if(evt.getSource()==hydrophobicityColour) - hydrophobicityColour_actionPerformed(); - else if(evt.getSource()==helixColour) - helixColour_actionPerformed(); - else if(evt.getSource()==strandColour) - strandColour_actionPerformed(); - else if(evt.getSource()==turnColour) - turnColour_actionPerformed(); - else if(evt.getSource()==buriedColour) - buriedColour_actionPerformed(); - else if(evt.getSource()==nucleotideColour) - nucleotideColour_actionPerformed(); - else if(evt.getSource()==modifyPID) + 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(evt.getSource()==modifyConservation) + else if(source==modifyConservation) modifyConservation_actionPerformed(); - else if(evt.getSource()==userDefinedColour) - userDefinedColour_actionPerformed(); - else if(evt.getSource()==PIDColour) - PIDColour_actionPerformed(); - else if(evt.getSource()==BLOSUM62Colour) - BLOSUM62Colour_actionPerformed(); - else if(evt.getSource()==sortPairwiseMenuItem) + 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(evt.getSource()==sortIDMenuItem) + else if(source==sortIDMenuItem) sortIDMenuItem_actionPerformed(); - else if(evt.getSource()==sortGroupMenuItem) + else if(source==sortGroupMenuItem) sortGroupMenuItem_actionPerformed(); - else if(evt.getSource()==removeRedundancyMenuItem) + else if(source==removeRedundancyMenuItem) removeRedundancyMenuItem_actionPerformed(); - else if(evt.getSource()==pairwiseAlignmentMenuItem) + else if(source==pairwiseAlignmentMenuItem) pairwiseAlignmentMenuItem_actionPerformed(); - else if(evt.getSource()==PCAMenuItem) + else if(source==PCAMenuItem) PCAMenuItem_actionPerformed(); - else if(evt.getSource()==averageDistanceTreeMenuItem) + else if(source==averageDistanceTreeMenuItem) averageDistanceTreeMenuItem_actionPerformed(); - else if(evt.getSource()==neighbourTreeMenuItem) + else if(source==neighbourTreeMenuItem) neighbourTreeMenuItem_actionPerformed(); - else if(evt.getSource()==njTreeBlosumMenuItem) + else if(source==njTreeBlosumMenuItem) njTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==avDistanceTreeBlosumMenuItem) + else if(source==avDistanceTreeBlosumMenuItem) avTreeBlosumMenuItem_actionPerformed(); - else if(evt.getSource()==documentation) + else if(source==documentation) documentation_actionPerformed(); - else if(evt.getSource()==about) + else if(source==about) about_actionPerformed(); } public void inputText_actionPerformed() { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -425,7 +648,7 @@ public void itemStateChanged(ItemEvent evt) protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet); + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, @@ -436,25 +659,136 @@ public void itemStateChanged(ItemEvent evt) 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 void outputAnnotations() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Annotations", + 600, 500); + cap.setText( new AnnotationFile().printAnnotations( + viewport.alignment.getAlignmentAnnotation() ) ); + } + + public void outputFeatures() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); + Frame frame = new Frame(); + frame.add(cap); + jalview.bin.JalviewLite.addFrame(frame, + "Features", + 600, 500); + + cap.setText(new FeaturesFile().printJalviewFormat( + viewport.alignment.getSequencesArray(), + viewport.featuresDisplayed)); + } + + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open="+ + appendProtocol( viewport.applet.getParameter("file") ) ); + + if(viewport.applet.getParameter("features")!=null) + { + url.append( "&features=" ); + url.append( appendProtocol( viewport.applet.getParameter("features") ) ); + } + + if(viewport.applet.getParameter("annotations")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("annotations") ) ); + } + + if(viewport.applet.getParameter("jnetfile")!=null) + { + url.append( "&annotations=" ); + url.append( appendProtocol( viewport.applet.getParameter("jnetfile") ) ); + } + + if(viewport.applet.getParameter("defaultColour")!=null) + { + url.append("&colour=" + + removeWhiteSpace(viewport.applet.getParameter("defaultColour")) + ); + } + + if(viewport.applet.getParameter("userDefinedColour")!=null) + { + 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) + { + url = viewport.applet.getCodeBase()+url; + } + return url; + } + public void closeMenuItem_actionPerformed() { - PaintRefresher.components.remove(viewport.alignment); - if(PaintRefresher.components.size()==0 && applet==null) + PaintRefresher.RemoveComponent(alignPanel); + PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas); + + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); this.dispose(); } - Stack historyList = new Stack(); - Stack redoList = new Stack(); + /** + * DOCUMENT ME! + */ void updateEditMenuBar() { - if (historyList.size() > 0) + + if (viewport.historyList.size() > 0) { undoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) historyList.peek(); - undoMenuItem.setLabel("Undo " + hi.getDescription()); + CommandI command = (CommandI) viewport.historyList.peek(); + undoMenuItem.setLabel("Undo " + command.getDescription()); } else { @@ -462,11 +796,12 @@ public void itemStateChanged(ItemEvent evt) undoMenuItem.setLabel("Undo"); } - if (redoList.size() > 0) + if (viewport.redoList.size() > 0) { redoMenuItem.setEnabled(true); - HistoryItem hi = (HistoryItem) redoList.peek(); - redoMenuItem.setLabel("Redo " + hi.getDescription()); + + CommandI command = (CommandI) viewport.redoList.peek(); + redoMenuItem.setLabel("Redo " + command.getDescription()); } else { @@ -475,71 +810,97 @@ public void itemStateChanged(ItemEvent evt) } } - public void addHistoryItem(HistoryItem hi) + public void addHistoryItem(CommandI command) { - historyList.push(hi); - updateEditMenuBar(); + if(command.getSize()>0) + { + viewport.historyList.push(command); + viewport.redoList.removeAllElements(); + updateEditMenuBar(); + viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + } } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void undoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, - HistoryItem.HIDE)); - restoreHistoryItem(hi); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + if(viewport.historyList.size()<1) + return; + + CommandI command = (CommandI)viewport.historyList.pop(); + viewport.redoList.push(command); + command.undoCommand(); + + AlignViewport originalSource = getOriginatingSource(command); + + originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null; + updateEditMenuBar(); + originalSource.firePropertyChange("alignment", null,originalSource.alignment.getSequences()); } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ protected void redoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) redoList.pop(); - restoreHistoryItem(hi); + 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; + updateEditMenuBar(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + originalSource.firePropertyChange("alignment", null, originalSource.alignment.getSequences()); } - // used by undo and redo - void restoreHistoryItem(HistoryItem hi) + AlignViewport getOriginatingSource(CommandI command) { - if (hi.getType() == HistoryItem.SORT) + 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; + if (command instanceof EditCommand) { - for (int i = 0; i < hi.getSequences().size(); i++) - { - viewport.alignment.getSequences().setElementAt(hi.getSequences(). - elementAt(i), i); - } - } - else - { - for (int i = 0; i < hi.getSequences().size(); i++) - { - SequenceI restore = (SequenceI) hi.getSequences().elementAt(i); - if (restore.getLength() == 0) - { - // log.System.out.println(hi.getHidden().elementAt(i)); - restore.setSequence(hi.getHidden().elementAt(i).toString()); - viewport.alignment.getSequences().insertElementAt( - restore, - hi.getAlignIndex(i)); - } - else - { - restore.setSequence(hi.getHidden().elementAt(i).toString()); - } - } - if (hi.getType() == HistoryItem.PASTE) + EditCommand editCommand = (EditCommand) command; + al = editCommand.getAlignment(); + Vector comps = (Vector) PaintRefresher.components + .get(viewport.getSequenceSetId()); + for (int i = 0; i < comps.size(); i++) { - for (int i = viewport.alignment.getHeight() - 1; - i > hi.getSequences().size() - 1; i--) + if (comps.elementAt(i) instanceof AlignmentPanel) { - viewport.alignment.deleteSequence(i); + if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment) + { + originalSource = ( (AlignmentPanel) comps.elementAt(i)).av; + break; + } } } } - updateEditMenuBar(); + if (originalSource == null) + { + //The original view is closed, we must validate + //the current view against the closed view first + if (al != null) + PaintRefresher.validateSequences(al, viewport.alignment); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + originalSource = viewport; + } + + + return originalSource; } public void moveSelectedSequences(boolean up) @@ -555,13 +916,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(null).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(null).contains(temp)) { continue; } @@ -575,13 +936,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(viewport.hiddenRepSequences).contains(temp)) { continue; } @@ -594,7 +955,8 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } - StringBuffer copiedSequences; + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) @@ -615,6 +977,25 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; + if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null) + { + copiedHiddenColumns = new Vector(); + int hiddenOffset = viewport.getSelectionGroup().getStartRes(); + for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size(); + i++) + { + int[] region = (int[]) + viewport.getColumnSelection().getHiddenColumns().elementAt(i); + + copiedHiddenColumns.addElement(new int[] + {region[0] - hiddenOffset, + region[1] - hiddenOffset}); + } + } + else + copiedHiddenColumns = null; + + for (int i = 0; i < sg.getSize(); i++) { SequenceI seq = null; @@ -659,7 +1040,7 @@ public void itemStateChanged(ItemEvent evt) copiedSequences.append(seq.getName() + "\t" + startRes + "\t" + endRes + "\t" + - seq.getSequence(sg.getStartRes(), + seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1) + "\n"); } @@ -672,8 +1053,6 @@ public void itemStateChanged(ItemEvent evt) protected void pasteThis_actionPerformed() { - addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, - HistoryItem.PASTE)); paste(false); } @@ -681,6 +1060,7 @@ public void itemStateChanged(ItemEvent evt) { try { + if (copiedSequences == null) { return; @@ -693,26 +1073,16 @@ public void itemStateChanged(ItemEvent evt) String name = st.nextToken(); int start = Integer.parseInt(st.nextToken()); int end = Integer.parseInt(st.nextToken()); - Sequence sequence = new Sequence(name, st.nextToken(), start, end); - - if (!newAlignment) - { - viewport.alignment.addSequence(sequence); - } - else - { - seqs.addElement(sequence); - } + seqs.addElement(new Sequence(name, st.nextToken(), start, end)); + } + SequenceI[] newSeqs = new SequenceI[seqs.size()]; + for (int i = 0; i < seqs.size(); i++) + { + newSeqs[i] = (SequenceI) seqs.elementAt(i); } if (newAlignment) { - SequenceI[] newSeqs = new SequenceI[seqs.size()]; - for (int i = 0; i < seqs.size(); i++) - { - newSeqs[i] = (SequenceI) seqs.elementAt(i); - } - String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { @@ -722,16 +1092,26 @@ public void itemStateChanged(ItemEvent evt) { newtitle = newtitle.concat("- from " + getTitle()); } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle); + AlignFrame af = new AlignFrame(new Alignment(newSeqs), + viewport.applet, + newtitle, + false); + if (copiedHiddenColumns != null) + { + for (int i = 0; i < copiedHiddenColumns.size(); i++) + { + int[] region = (int[]) copiedHiddenColumns.elementAt(i); + af.viewport.hideColumns(region[0], region[1]); + } + } + - jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); + jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH, + DEFAULT_HEIGHT); } else { - viewport.setEndSeq(viewport.alignment.getHeight()); - viewport.alignment.getWidth(); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + addSequences(newSeqs); } } @@ -740,6 +1120,30 @@ 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(); @@ -748,62 +1152,62 @@ public void itemStateChanged(ItemEvent evt) protected void delete_actionPerformed() { - addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, - HistoryItem.HIDE)); - if (viewport.getSelectionGroup() == null) + + SequenceGroup sg = viewport.getSelectionGroup(); + if (sg == null) { return; } + Vector seqs = new Vector(); + SequenceI seq; + for (int i = 0; i < sg.getSize(); i++) + { + seq = sg.getSequenceAt(i); + seqs.addElement(seq); + } - SequenceGroup sg = viewport.getSelectionGroup(); - boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) - allSequences = true; - for (int i = 0; i < sg.sequences.size(); i++) - { - SequenceI seq = sg.getSequenceAt(i); - int index = viewport.getAlignment().findIndex(seq); - seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1); + // 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 (allSequences) - { - viewport.getColumnSelection().removeElements(sg.getStartRes(), - sg.getEndRes() + 1); - } + SequenceI [] cut = new SequenceI[seqs.size()]; + for(int i=0; i 0) { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, - HistoryItem.HIDE)); - int min = colSel.getMin(); - viewport.getAlignment().trimLeft(min); - colSel.compensateForEdit(0, min); + if(trimLeft) + column = colSel.getMin(); + else + column = colSel.getMax(); - if (viewport.getSelectionGroup() != null) - { - viewport.getSelectionGroup().adjustForRemoveLeft(min); - } + SequenceI [] seqs; + if(viewport.getSelectionGroup()!=null) + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); + else + seqs = viewport.alignment.getSequencesArray(); - Vector groups = viewport.alignment.getGroups(); - for (int i = 0; i < groups.size(); i++) - { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveLeft(min)) - { - viewport.alignment.deleteGroup(sg); - } - } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } - } - public void remove2RightMenuItem_actionPerformed() - { - ColumnSelection colSel = viewport.getColumnSelection(); - if (colSel.size() > 0) - { - addHistoryItem(new HistoryItem("Remove Right", viewport.alignment, - HistoryItem.HIDE)); - int max = colSel.getMax(); - viewport.getAlignment().trimRight(max); - if (viewport.getSelectionGroup() != null) + TrimRegionCommand trimRegion; + if(trimLeft) { - viewport.getSelectionGroup().adjustForRemoveRight(max); + trimRegion = new TrimRegionCommand("Remove Left", + 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."); + + + addHistoryItem(trimRegion); Vector groups = viewport.alignment.getGroups(); + for (int i = 0; i < groups.size(); i++) { SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (!sg.adjustForRemoveRight(max)) + + if ( (trimLeft && !sg.adjustForRemoveLeft(column)) + || (!trimLeft && !sg.adjustForRemoveRight(column))) { viewport.alignment.deleteGroup(sg); } } - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + } } + public void removeGappedColumnMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gapped Columns", - viewport.alignment, - HistoryItem.HIDE)); + int start = 0, end = viewport.alignment.getWidth()-1; - //This is to maintain viewport position on first residue - //of first sequence - SequenceI seq = viewport.alignment.getSequenceAt(0); - int startRes = seq.findPosition(viewport.startRes); + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) + { + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); + start = viewport.getSelectionGroup().getStartRes(); + end = viewport.getSelectionGroup().getEndRes(); + } + else + seqs = viewport.alignment.getSequencesArray(); - viewport.getAlignment().removeGaps(); - viewport.setStartRes(seq.findIndex(startRes)-1); + RemoveGapColCommand removeGapCols = + new RemoveGapColCommand("Remove Gapped Columns", + seqs, + start, end, + viewport.getGapCharacter()); - viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); - } + addHistoryItem(removeGapCols); - public void removeAllGapsMenuItem_actionPerformed() - { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, - HistoryItem.HIDE)); + 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()); - SequenceI current; - int jSize; - - Vector seqs=null; + } - int start=0, end = viewport.alignment.getWidth(); + public void removeAllGapsMenuItem_actionPerformed() + { + int start = 0, end = viewport.alignment.getWidth()-1; - if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + SequenceI[] seqs; + if (viewport.getSelectionGroup() != null) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.hiddenRepSequences); start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes()+1; + end = viewport.getSelectionGroup().getEndRes(); } else - seqs = viewport.alignment.getSequences(); + seqs = viewport.alignment.getSequencesArray(); - for (int i = 0; i < seqs.size(); i++) - { - current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; + addHistoryItem(new RemoveGapsCommand("Remove Gaps", + seqs, + start, end, + viewport.getGapCharacter())); - do - { - if (jalview.util.Comparison.isGap(current.getCharAt(j))) - { - if(rangeStart==-1) - { - rangeStart = j; - rangeEnd = j+1; - } - else - { - rangeEnd++; - } - j++; - } - else - { - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - j-=rangeEnd-rangeStart; - jSize-=rangeEnd-rangeStart; - rangeStart = -1; - rangeEnd = -1; - } - else - j++; - } - } - while (j < end && j < jSize); - if(rangeStart>-1) - { - current.deleteChars(rangeStart, rangeEnd); - } - } viewport.setStartRes(seq.findIndex(startRes)-1); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); + } - public void alignmentChanged() + public void findMenuItem_actionPerformed() { - viewport.updateConsensus(); - viewport.updateConservation (); - resetAllColourSchemes(); - if(alignPanel.overviewPanel!=null) - alignPanel.overviewPanel.updateOverviewImage(); - - viewport.alignment.adjustSequenceAnnotations(); - alignPanel.repaint(); + new Finder(alignPanel); } - void resetAllColourSchemes() + public void newView() { - ColourSchemeI cs = viewport.globalColourScheme; - if(cs!=null) + AlignmentI newal; + if (viewport.hasHiddenRows) + newal = new Alignment(viewport.getAlignment(). + getHiddenSequences() + .getFullAlignment(). + getSequencesArray()); + else + newal = new Alignment(viewport.alignment.getSequencesArray()); + + AlignFrame newaf = new AlignFrame(newal, + viewport.applet, + "", + false); + + newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId(); + PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel, + newaf.alignPanel.av.getSequenceSetId()); + + PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas, + newaf.alignPanel.av.getSequenceSetId()); + PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas, + newaf.alignPanel.av.getSequenceSetId()); + + Vector comps = (Vector)PaintRefresher.components.get(viewport.getSequenceSetId()); + int viewSize = -1; + for (int i = 0; i < comps.size(); i++) { - if (cs instanceof ClustalxColourScheme) - { - ( (ClustalxColourScheme) viewport.getGlobalColourScheme()). - resetClustalX(viewport.alignment.getSequences(), - viewport.alignment.getWidth()); - } - - cs.setConsensus(viewport.vconsensus); - if (cs.conservationApplied()) - { - Alignment al = (Alignment) viewport.alignment; - Conservation c = new Conservation("All", - ResidueProperties.propHash, 3, - al.getSequences(), 0, - al.getWidth() - 1); - c.calculate(); - c.verdict(false, viewport.ConsPercGaps); - - cs.setConservation(c); - } + if (comps.elementAt(i) instanceof AlignmentPanel) + viewSize++; } - int s, sSize = viewport.alignment.getGroups().size(); - for(s=0; s -1) + title = title.substring(0, title.indexOf("(View")); + title+= "(View "+viewSize+")"; + newaf.setTitle(title.toString()); - public void findMenuItem_actionPerformed() - { - new Finder(alignPanel); - } - public void font_actionPerformed() - { - new FontChooser(alignPanel); - } + newaf.viewport.historyList = viewport.historyList; + newaf.viewport.redoList = viewport.redoList; + + } public void seqLimits_itemStateChanged() @@ -1084,52 +1466,6 @@ public void itemStateChanged(ItemEvent evt) alignPanel.repaint(); } - protected void scaleAbove_actionPerformed() - { - viewport.setScaleAboveWrapped(scaleAbove.getState()); - alignPanel.repaint(); - } - - protected void scaleLeft_actionPerformed() - { - viewport.setScaleLeftWrapped(scaleLeft.getState()); - alignPanel.repaint(); - } - - protected void scaleRight_actionPerformed() - { - viewport.setScaleRightWrapped(scaleRight.getState()); - alignPanel.repaint(); - } - - public void viewBoxesMenuItem_actionPerformed() - { - viewport.setShowBoxes(viewBoxesMenuItem.getState()); - alignPanel.repaint(); - } - - public void viewTextMenuItem_actionPerformed() - { - viewport.setShowText(viewTextMenuItem.getState()); - alignPanel.repaint(); - } - - protected void renderGapsMenuItem_actionPerformed() - { - viewport.setRenderGaps(renderGapsMenuItem.getState()); - alignPanel.repaint(); - } - - public void annotationPanelMenuItem_actionPerformed() - { - viewport.setShowAnnotation(annotationPanelMenuItem.getState()); - alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); - } - - public void featureSettings_actionPerformed() - { - new FeatureSettings(viewport, alignPanel); - } public void overviewMenuItem_actionPerformed() { @@ -1159,62 +1495,6 @@ public void itemStateChanged(ItemEvent evt) } - protected void noColourmenuItem_actionPerformed() - { - changeColour(null); - } - - public void clustalColour_actionPerformed() - { - abovePIDThreshold.setState(false); - changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), - viewport.alignment.getWidth())); - } - - public void zappoColour_actionPerformed() - { - changeColour(new ZappoColourScheme()); - } - - public void taylorColour_actionPerformed() - { - changeColour(new TaylorColourScheme()); - } - - public void hydrophobicityColour_actionPerformed() - { - changeColour(new HydrophobicColourScheme()); - } - - public void helixColour_actionPerformed() - { - changeColour(new HelixColourScheme()); - } - - public void strandColour_actionPerformed() - { - changeColour(new StrandColourScheme()); - } - - public void turnColour_actionPerformed() - { - changeColour(new TurnColourScheme()); - } - - public void buriedColour_actionPerformed() - { - changeColour(new BuriedColourScheme()); - } - - public void nucleotideColour_actionPerformed() - { - changeColour(new NucleotideColourScheme()); - } - - protected void applyToAllGroups_actionPerformed() - { - viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); - } void changeColour(ColourSchemeI cs) { @@ -1258,7 +1538,7 @@ public void itemStateChanged(ItemEvent evt) cs.setConservation(null); } - cs.setConsensus(viewport.vconsensus); + cs.setConsensus(viewport.hconsensus); } viewport.setGlobalColourScheme(cs); @@ -1277,7 +1557,9 @@ public void itemStateChanged(ItemEvent evt) } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(viewport.hiddenRepSequences), + sg.getWidth()); } else { @@ -1297,7 +1579,8 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1306,7 +1589,7 @@ public void itemStateChanged(ItemEvent evt) { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(viewport.hiddenRepSequences), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1376,42 +1659,29 @@ public void itemStateChanged(ItemEvent evt) modifyPID_actionPerformed(); } - public void userDefinedColour_actionPerformed() - { - new UserDefinedColours(alignPanel, null); - } - - public void PIDColour_actionPerformed() - { - changeColour(new PIDColourScheme()); - } - public void BLOSUM62Colour_actionPerformed() - { - changeColour(new Blosum62ColourScheme()); - } public void sortPairwiseMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, - HistoryItem.SORT)); + SequenceI [] oldOrder = viewport.getAlignment().getSequencesArray(); AlignmentSorter.sortByPID(viewport.getAlignment(), viewport.getAlignment().getSequenceAt(0)); + addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder, viewport.alignment)); alignPanel.repaint(); } 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(); } 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(); @@ -1419,17 +1689,13 @@ public void itemStateChanged(ItemEvent evt) public void removeRedundancyMenuItem_actionPerformed() { - RedundancyPanel sp = new RedundancyPanel(alignPanel); - Frame frame = new Frame(); - frame.add(sp); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 120); - + new RedundancyPanel(alignPanel); } public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize() > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1493,7 +1759,7 @@ 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) @@ -1518,26 +1784,42 @@ public void itemStateChanged(ItemEvent evt) } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else + if ( (viewport.getSelectionGroup() != null && + viewport.getSelectionGroup().getSize() > 1) + || (viewport.getSelectionGroup() == null + && viewport.alignment.getHeight() > 1)) { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); + final TreePanel tp = new TreePanel(viewport, + type, + pwType); + + addTreeMenuItem(tp, title); + + jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } + } - addTreeMenuItem(tp, title); + 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); + } - jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); + public void loadTree(jalview.io.NewickFile tree, String treeFile) + { + TreePanel tp = new TreePanel(viewport, + treeFile, + "From File - ", + tree); + jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); + addTreeMenuItem(tp, treeFile); } - public void addTreeMenuItem(final TreePanel treePanel, String title) + void addTreeMenuItem(final TreePanel treePanel, String title) { final MenuItem item = new MenuItem(title); sortByTreeMenu.add(item); @@ -1545,8 +1827,8 @@ 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(); } @@ -1597,7 +1879,7 @@ public void itemStateChanged(ItemEvent evt) g.drawString("If you use JalView, please cite:", x, y += fh + 8); g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", x, y += fh); - g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh); + g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); } } @@ -1633,7 +1915,7 @@ public void itemStateChanged(ItemEvent evt) public void showURL(String url, String target) { - if (applet == null) + if (viewport.applet == null) { System.out.println("Not running as applet - no browser available."); } @@ -1641,7 +1923,8 @@ public void itemStateChanged(ItemEvent evt) { try { - applet.getAppletContext().showDocument(new java.net.URL(url), + System.out.println("Show url: "+url); + viewport.applet.getAppletContext().showDocument(new java.net.URL(url), target); } catch (Exception ex) @@ -1656,15 +1939,21 @@ public void itemStateChanged(ItemEvent evt) //JBuilder Graphics here protected MenuBar alignFrameMenuBar = new MenuBar(); - protected Menu fileMenu = new Menu(); - protected MenuItem closeMenuItem = new MenuItem(); - protected Menu editMenu = new Menu(); - protected Menu viewMenu = new Menu(); - protected Menu colourMenu = new Menu(); - protected Menu calculateMenu = new Menu(); - protected MenuItem selectAllSequenceMenuItem = new MenuItem(); - protected MenuItem deselectAllSequenceMenuItem = new MenuItem(); - protected MenuItem invertSequenceMenuItem = new MenuItem(); + 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(); @@ -1705,8 +1994,7 @@ public void itemStateChanged(ItemEvent evt) protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); MenuItem findMenuItem = new MenuItem(); - Menu searchMenu = new Menu(); - protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); protected MenuItem nucleotideColour = new MenuItem(); MenuItem deleteGroups = new MenuItem(); MenuItem delete = new MenuItem(); @@ -1722,6 +2010,8 @@ public void itemStateChanged(ItemEvent evt) 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(); @@ -1732,8 +2022,9 @@ public void itemStateChanged(ItemEvent evt) protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); Panel embeddedMenu; Label embeddedEdit; - Label embeddedSearch; + Label embeddedSelect; Label embeddedView; + Label embeddedFormat; Label embeddedColour; Label embeddedFile; Label embeddedHelp; @@ -1747,12 +2038,11 @@ public void itemStateChanged(ItemEvent evt) MenuItem item; // dynamically fill save as menu with available formats - for (int i = 0; i < jalview.io.AppletFormatAdapter.formats.size(); i++) + for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++) { - item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. - elementAt( - i)); + item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]); + item.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -1763,19 +2053,15 @@ public void itemStateChanged(ItemEvent evt) outputTextboxMenu.add(item); } - - fileMenu.setLabel("File"); - closeMenuItem.setLabel("Close"); closeMenuItem.addActionListener(this); - editMenu.setLabel("Edit"); - viewMenu.setLabel("View"); - colourMenu.setLabel("Colour"); - calculateMenu.setLabel("Calculate"); - selectAllSequenceMenuItem.setLabel("Select all"); + loadApplication.addActionListener(this); + + loadTree.addActionListener(this); + loadAnnotations.addActionListener(this); + outputFeatures.addActionListener(this); + outputAnnotations.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); - deselectAllSequenceMenuItem.setLabel("Deselect All"); deselectAllSequenceMenuItem.addActionListener(this); - invertSequenceMenuItem.setLabel("Invert Selection"); invertSequenceMenuItem.addActionListener(this); remove2LeftMenuItem.setLabel("Remove Left"); remove2LeftMenuItem.addActionListener(this); @@ -1808,7 +2094,6 @@ public void itemStateChanged(ItemEvent evt) 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"); @@ -1864,9 +2149,7 @@ public void itemStateChanged(ItemEvent evt) renderGapsMenuItem.addItemListener(this); findMenuItem.setLabel("Find..."); findMenuItem.addActionListener(this); - searchMenu.setLabel("Search"); - - abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.setLabel("Above Identity Threshold"); abovePIDThreshold.addItemListener(this); nucleotideColour.setLabel("Nucleotide"); nucleotideColour.addActionListener(this); @@ -1907,6 +2190,7 @@ public void itemStateChanged(ItemEvent evt) sortByTreeMenu.setLabel("By Tree Order"); sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); @@ -1923,19 +2207,50 @@ public void itemStateChanged(ItemEvent evt) featureSettings.addActionListener(this); sequenceFeatures.setLabel("Sequence Features"); sequenceFeatures.addItemListener(this); - sequenceFeatures.setState(true); - + sequenceFeatures.setState(false); + annotationColour.setLabel("by Annotation..."); + annotationColour.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Sequence Selection"); + invertColSel.setLabel("Invert Column Selection"); + menu1.setLabel("Show"); + showColumns.setLabel("All Columns "); + showSeqs.setLabel("All Sequences"); + menu2.setLabel("Hide"); + hideColumns.setLabel("Selected Columns"); + hideSequences.setLabel("Selected Sequences"); + invertColSel.addActionListener(this); + showColumns.addActionListener(this); + showSeqs.addActionListener(this); + hideColumns.addActionListener(this); + hideSequences.addActionListener(this); + formatMenu.setLabel("Format"); + selectMenu.setLabel("Select"); + newView.setLabel("New View"); + newView.addActionListener(this); alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); - alignFrameMenuBar.add(searchMenu); - alignFrameMenuBar.add(viewMenu); - alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(selectMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(formatMenu); + alignFrameMenuBar.add(colourMenu); 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); @@ -1943,31 +2258,20 @@ public void itemStateChanged(ItemEvent evt) editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); - editMenu.add(selectAllSequenceMenuItem); - editMenu.add(deselectAllSequenceMenuItem); - editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); - editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); editMenu.add(removeGappedColumnMenuItem); editMenu.add(removeAllGapsMenuItem); editMenu.add(removeRedundancyMenuItem); - searchMenu.add(findMenuItem); - viewMenu.add(font); - viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.addSeparator(); - viewMenu.add(wrapMenuItem); - viewMenu.add(scaleAbove); - viewMenu.add(scaleLeft); - viewMenu.add(scaleRight); - viewMenu.addSeparator(); - viewMenu.add(viewBoxesMenuItem); - viewMenu.add(viewTextMenuItem); - viewMenu.add(colourTextMenuItem); - viewMenu.add(renderGapsMenuItem); - viewMenu.add(annotationPanelMenuItem); + viewMenu.add(newView); + viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); + viewMenu.add(annotationPanelMenuItem); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); @@ -1990,11 +2294,13 @@ public void itemStateChanged(ItemEvent evt) colourMenu.add(modifyConservation); colourMenu.add(abovePIDThreshold); colourMenu.add(modifyPID); - calculateMenu.add(sort); + 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); @@ -2008,40 +2314,57 @@ public void itemStateChanged(ItemEvent evt) calculate.add(njTreeBlosumMenuItem); helpMenu.add(documentation); helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + formatMenu.add(font); + formatMenu.add(seqLimits); + formatMenu.add(wrapMenuItem); + formatMenu.add(scaleAbove); + formatMenu.add(scaleLeft); + formatMenu.add(scaleRight); + formatMenu.add(viewBoxesMenuItem); + formatMenu.add(viewTextMenuItem); + formatMenu.add(colourTextMenuItem); + formatMenu.add(renderGapsMenuItem); + selectMenu.add(findMenuItem); + selectMenu.addSeparator(); + selectMenu.add(selectAllSequenceMenuItem); + selectMenu.add(deselectAllSequenceMenuItem); + selectMenu.add(invertSequenceMenuItem); + selectMenu.add(invertColSel); + selectMenu.add(deleteGroups); } public void setEmbedded() { embeddedMenu = new Panel(); - embeddedEdit = new Label(); - embeddedSearch = new Label(); - embeddedView = new Label(); - embeddedColour = new Label(); - embeddedFile = new Label(); - embeddedHelp = new Label(); - embeddedCalculate = new Label(); + embeddedEdit = new Label("Edit"); + embeddedSelect = new Label("Select"); + embeddedView = new Label("View"); + embeddedFormat = new Label("Format"); + embeddedColour = new Label("Colour"); + embeddedFile = new Label("File"); + embeddedHelp = new Label("Help"); + embeddedCalculate = new Label("Calculate"); flowLayout1 = new FlowLayout(); embeddedMenu.setBackground(Color.lightGray); embeddedMenu.setLayout(flowLayout1); - embeddedEdit.setText("Edit"); embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedSearch.setText("Search"); - embeddedSearch.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedView.setText("View"); + embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedColour.setText("Colour"); + embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedFile.setText("File"); embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedHelp.setText("Help"); embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); - embeddedCalculate.setText("Calculate"); embeddedMenu.add(embeddedFile); embeddedMenu.add(embeddedEdit); - embeddedMenu.add(embeddedSearch); + embeddedMenu.add(embeddedSelect); embeddedMenu.add(embeddedView); + embeddedMenu.add(embeddedFormat); embeddedMenu.add(embeddedColour); embeddedMenu.add(embeddedCalculate); embeddedMenu.add(embeddedHelp); @@ -2050,35 +2373,45 @@ public void itemStateChanged(ItemEvent evt) flowLayout1.setVgap(0); embeddedFile.addMouseListener(this); embeddedEdit.addMouseListener(this); - embeddedSearch.addMouseListener(this); + embeddedSelect.addMouseListener(this); embeddedView.addMouseListener(this); + embeddedFormat.addMouseListener(this); embeddedColour.addMouseListener(this); embeddedCalculate.addMouseListener(this); embeddedHelp.addMouseListener(this); - setVisible(false); fileMenu.remove(closeMenuItem); - fileMenu.remove(2); // Seperator + fileMenu.remove(3); // Seperator - applet.setLayout(new BorderLayout()); - applet.add(embeddedMenu, BorderLayout.NORTH); - applet.add(statusBar, BorderLayout.SOUTH); - applet.validate(); + viewport.applet.setLayout(new BorderLayout()); + viewport.applet.add(embeddedMenu, BorderLayout.NORTH); + viewport.applet.add(statusBar, BorderLayout.SOUTH); - - alignPanel.setSize(applet.size().width, applet.size().height + alignPanel.setSize(viewport.applet.size().width, viewport.applet.size().height - embeddedMenu.HEIGHT - statusBar.HEIGHT); - applet.add(alignPanel, BorderLayout.CENTER); - applet.validate(); + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); + } PopupMenu filePopup, editPopup, searchPopup, - viewPopup, colourPopup, calculatePopup, helpPopup; + viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup; MenuItem featureSettings = new MenuItem(); CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + MenuItem annotationColour = new MenuItem(); + MenuItem invertColSel = new MenuItem(); + Menu menu1 = new Menu(); + MenuItem showColumns = new MenuItem(); + MenuItem showSeqs = new MenuItem(); + Menu menu2 = new Menu(); + MenuItem hideColumns = new MenuItem(); + MenuItem hideSequences = new MenuItem(); + Menu formatMenu = new Menu(); + Menu selectMenu = new Menu(); + MenuItem newView = new MenuItem(); public void mousePressed(MouseEvent evt) { @@ -2092,14 +2425,18 @@ public void itemStateChanged(ItemEvent evt) { popup = editPopup = genPopupMenu(editPopup, editMenu); } - else if(source==embeddedSearch) + else if(source==embeddedSelect) { - popup = searchPopup = genPopupMenu(searchPopup, searchMenu); + popup = searchPopup = genPopupMenu(searchPopup, selectMenu); } else if(source==embeddedView) { popup = viewPopup = genPopupMenu(viewPopup, viewMenu); } + else if (source ==embeddedFormat) + { + popup = formatPopup = genPopupMenu(formatPopup, formatMenu); + } else if(source==embeddedColour) { popup = colourPopup = genPopupMenu(colourPopup, colourMenu);