X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=86c079c115b07702f843488f0006a9f3ea8d825c;hb=e6879a932d0144d64a5ab703ae311aed0eeb83e5;hp=cf4c40df44831919c95f4dd2c8b63e8272ca4347;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index cf4c40d..86c079c 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 @@ -31,62 +31,48 @@ import java.io.BufferedReader; import java.net.URL; -public class AlignFrame extends Frame +public class AlignFrame extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener { - final AlignmentPanel alignPanel; - public final AlignViewport viewport; + public AlignmentPanel alignPanel; + public AlignViewport viewport; int NEW_WINDOW_WIDTH = 700; int NEW_WINDOW_HEIGHT = 500; - jalview.bin.JalviewLite applet; + String jalviewServletURL; - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) + + public AlignFrame(AlignmentI al, + jalview.bin.JalviewLite applet, + String title, + boolean embedded) { + + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + try{ jbInit(); }catch(Exception ex) { ex.printStackTrace(); } - this.applet = applet; + viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - if(applet!=null) - { - String treeFile = applet.getParameter("treeFile"); - if (treeFile != null) - { - try - { - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); + annotationPanelMenuItem.setState(viewport.showAnnotation); - if (fin.getTree() != null) - { - TreePanel tp = null; - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - fin, "FromFile", applet.getCodeBase() + treeFile); - jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); - addTreeMenuItem(tp, treeFile); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + seqLimits.setState(viewport.showJVSuffix); + if(applet!=null) + { String param = applet.getParameter("sortBy"); if (param != null) { if (param.equalsIgnoreCase("Id")) - sortIDMenuItem_actionPerformed(null); + sortIDMenuItem_actionPerformed(); else if (param.equalsIgnoreCase("Pairwise Identity")) - sortPairwiseMenuItem_actionPerformed(null); + sortPairwiseMenuItem_actionPerformed(); } param = applet.getParameter("wrap"); @@ -95,7 +81,7 @@ public class AlignFrame extends Frame if (param.equalsIgnoreCase("true")) { wrapMenuItem.setState(true); - wrapMenuItem_actionPerformed(null); + wrapMenuItem_actionPerformed(); } } @@ -119,13 +105,13 @@ public class AlignFrame extends Frame } - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent e) - { - closeMenuItem_actionPerformed(null); - } - }); + //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); viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener() { @@ -138,13 +124,20 @@ public class AlignFrame extends Frame } }); - jalview.bin.JalviewLite.addFrame(this, title, - NEW_WINDOW_WIDTH, - NEW_WINDOW_HEIGHT); - + if(embedded) + { + setEmbedded(); + } + else + { + add(alignPanel, BorderLayout.CENTER); + jalview.bin.JalviewLite.addFrame(this, title, NEW_WINDOW_WIDTH, + NEW_WINDOW_HEIGHT); + } + alignPanel.validate(); + alignPanel.repaint(); } - public AlignViewport getAlignViewport() { return viewport; @@ -162,85 +155,403 @@ public class AlignFrame extends Frame * @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); + ex.printStackTrace(); + } - BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); - SequenceI seq = null; - String line, type, desc, token; + if(featuresFile) + { + if(featureLinks.size()>0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; + viewport.showSequenceFeatures = true; + sequenceFeatures.setState(true); + alignPanel.repaint(); + } - 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) + } + + + 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 + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) { - type = st.nextToken(); - UserColourScheme ucs = new UserColourScheme(st.nextToken()); - fr.setColour(type, ucs.findColour("A")); - continue; + cut_actionPerformed(); } + 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()) + { + paste(true); + } + break; + case KeyEvent.VK_A: + if (evt.isControlDown() || evt.isMetaDown()) + { + selectAllSequenceMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_DOWN: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); + break; - while (st.hasMoreElements()) + case KeyEvent.VK_UP: + if (viewport.cursorMode) { - 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()); - } + 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; - start = Integer.parseInt(st.nextToken()); - end = Integer.parseInt(st.nextToken()); + 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; - seq = viewport.alignment.getSequenceAt(index); - start = seq.findIndex(start) - 1; - end = seq.findIndex(end) - 1; + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; - type = st.nextToken(); + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; - if(fr.getColour(type)==null) - { - // Probably the old style groups file - UserColourScheme ucs = new UserColourScheme(type); - fr.setColour(type, ucs.findColour("A")); - } + 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; + } + alignPanel.seqPanel.seqCanvas.repaint(); + break; - sf = new SequenceFeature(type, desc, "", start, end); + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_H: + { + boolean toggleSeqs = !evt.isControlDown(); + boolean toggleCols = !evt.isShiftDown(); + boolean hide = false; + SequenceGroup sg = viewport.getSelectionGroup(); - seq.addSequenceFeature(sf); + if(toggleSeqs) + { + if (sg != null && sg.getSize(false) != viewport.alignment.getHeight()) + { + hide = true; + viewport.hideAllSelectedSeqs(); + } + else if (!(toggleCols && viewport.colSel.getSelected().size() > 0)) + viewport.showAllHiddenSeqs(); } - } - viewport.showSequenceFeatures = true; + if(toggleCols) + { + if (viewport.colSel.getSelected().size() > 0) + { + viewport.hideSelectedColumns(); + if(!toggleSeqs) + viewport.selectionGroup = sg; + } + else if (!hide) + viewport.showAllHiddenColumns(); + } - alignPanel.repaint(); + alignPanel.repaint(); + break; + } } - catch (Exception ex) + } + 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) + scaleAbove_actionPerformed(); + else if(evt.getSource()==scaleLeft) + scaleLeft_actionPerformed(); + else if(evt.getSource()==scaleRight) + scaleRight_actionPerformed(); + else if(evt.getSource()==seqLimits) + seqLimits_itemStateChanged(); + else if(evt.getSource()==viewBoxesMenuItem) + viewBoxesMenuItem_actionPerformed(); + else if(evt.getSource()==viewTextMenuItem) + viewTextMenuItem_actionPerformed(); + else if(evt.getSource()==renderGapsMenuItem) + renderGapsMenuItem_actionPerformed(); + else if(evt.getSource()==annotationPanelMenuItem) + annotationPanelMenuItem_actionPerformed(); + 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) + applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); + } + public void actionPerformed(ActionEvent evt) + { + Object source = evt.getSource(); + + if(source==inputText) + inputText_actionPerformed(); + else if(source==loadTree) + loadTree_actionPerformed(); + else if(source==loadApplication) + launchFullApplication(); + else if(source==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(source==copy) + copy_actionPerformed(); + else if(source==undoMenuItem) + undoMenuItem_actionPerformed(); + 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) + remove2LeftMenuItem_actionPerformed(); + else if(source==remove2RightMenuItem) + remove2RightMenuItem_actionPerformed(); + else if(source==removeGappedColumnMenuItem) + removeGappedColumnMenuItem_actionPerformed(); + else if(source==removeAllGapsMenuItem) + removeAllGapsMenuItem_actionPerformed(); + else if(source==findMenuItem) + findMenuItem_actionPerformed(); + else if(source==font) + font_actionPerformed(); + else if(source==showColumns) { - System.out.println("Error parsing groups file: " + ex); + viewport.showAllHiddenColumns(); alignPanel.repaint(); } - } - - - public void inputText_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); + 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) + featureSettings_actionPerformed(); + else if(source==overviewMenuItem) + overviewMenuItem_actionPerformed(); + else if(source==noColourmenuItem) + noColourmenuItem_actionPerformed(); + else if(source==clustalColour) + clustalColour_actionPerformed(); + else if(source==zappoColour) + zappoColour_actionPerformed(); + else if(source==taylorColour) + taylorColour_actionPerformed(); + else if(source==hydrophobicityColour) + hydrophobicityColour_actionPerformed(); + else if(source==helixColour) + helixColour_actionPerformed(); + else if(source==strandColour) + strandColour_actionPerformed(); + else if(source==turnColour) + turnColour_actionPerformed(); + else if(source==buriedColour) + buriedColour_actionPerformed(); + else if(source==nucleotideColour) + nucleotideColour_actionPerformed(); + else if(source==modifyPID) + modifyPID_actionPerformed(); + else if(source==modifyConservation) + modifyConservation_actionPerformed(); + else if(source==userDefinedColour) + userDefinedColour_actionPerformed(); + else if(source==PIDColour) + PIDColour_actionPerformed(); + else if(source==BLOSUM62Colour) + BLOSUM62Colour_actionPerformed(); + 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() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -248,7 +559,7 @@ public class AlignFrame extends Frame protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, @@ -259,11 +570,82 @@ public class AlignFrame extends Frame viewport.showJVSuffix)); } - public void closeMenuItem_actionPerformed(ActionEvent e) + 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) + if(PaintRefresher.components.size()==0 && viewport.applet==null) System.exit(0); + + this.dispose(); } Stack historyList = new Stack(); @@ -299,21 +681,28 @@ public class AlignFrame extends Frame public void addHistoryItem(HistoryItem hi) { historyList.push(hi); + redoList.removeAllElements(); updateEditMenuBar(); } - protected void undoMenuItem_actionPerformed(ActionEvent e) + protected void undoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) historyList.pop(); - redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem nh,hi = (HistoryItem) historyList.pop(); + redoList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); restoreHistoryItem(hi); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - protected void redoMenuItem_actionPerformed(ActionEvent e) + protected void redoMenuItem_actionPerformed() { - HistoryItem hi = (HistoryItem) redoList.pop(); + HistoryItem nh,hi = (HistoryItem) redoList.pop(); + historyList.push(nh=new HistoryItem(hi.getDescription(), viewport.alignment, + HistoryItem.HIDE)); + if (hi.alColumnChanges!=null) + nh.alColumnChanges=hi.alColumnChanges.getInverse(); restoreHistoryItem(hi); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -322,42 +711,7 @@ public class AlignFrame extends Frame // used by undo and redo void restoreHistoryItem(HistoryItem hi) { - if (hi.getType() == HistoryItem.SORT) - { - 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) - { - for (int i = viewport.alignment.getHeight() - 1; - i > hi.getSequences().size() - 1; i--) - { - viewport.alignment.deleteSequence(i); - } - } - } - + hi.restore(viewport.getColumnSelection()); updateEditMenuBar(); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); @@ -376,13 +730,13 @@ public class AlignFrame extends Frame for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(false).contains(temp)) { continue; } @@ -396,13 +750,13 @@ public class AlignFrame extends Frame for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(true).contains(temp)) { continue; } @@ -415,8 +769,9 @@ public class AlignFrame extends Frame alignPanel.repaint(); } - StringBuffer copiedSequences; - protected void copy_actionPerformed(ActionEvent e) + static StringBuffer copiedSequences; + static Vector copiedHiddenColumns; + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -426,7 +781,7 @@ public class AlignFrame extends Frame SequenceGroup sg = viewport.getSelectionGroup(); copiedSequences = new StringBuffer(); Hashtable orderedSeqs = new Hashtable(); - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.alignment.findIndex(seq); @@ -436,7 +791,26 @@ public class AlignFrame extends Frame int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(); i++) + 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(false); i++) { SequenceI seq = null; @@ -486,12 +860,12 @@ public class AlignFrame extends Frame } - protected void pasteNew_actionPerformed(ActionEvent e) + protected void pasteNew_actionPerformed() { paste(true); } - protected void pasteThis_actionPerformed(ActionEvent e) + protected void pasteThis_actionPerformed() { addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment, HistoryItem.PASTE)); @@ -543,7 +917,19 @@ public class AlignFrame extends Frame { 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); @@ -561,13 +947,13 @@ public class AlignFrame extends Frame } - protected void cut_actionPerformed(ActionEvent e) + protected void cut_actionPerformed() { - copy_actionPerformed(null); - delete_actionPerformed(null); + copy_actionPerformed(); + delete_actionPerformed(); } - protected void delete_actionPerformed(ActionEvent e) + protected void delete_actionPerformed() { addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment, HistoryItem.HIDE)); @@ -579,10 +965,10 @@ public class AlignFrame extends Frame SequenceGroup sg = viewport.getSelectionGroup(); boolean allSequences = false; - if(sg.sequences.size()==viewport.alignment.getHeight()) + if(sg.getSize(false)==viewport.alignment.getHeight()) allSequences = true; - for (int i = 0; i < sg.sequences.size(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = sg.getSequenceAt(i); int index = viewport.getAlignment().findIndex(seq); @@ -622,7 +1008,7 @@ public class AlignFrame extends Frame } - protected void deleteGroups_actionPerformed(ActionEvent e) + protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); viewport.setSelectionGroup(null); @@ -630,7 +1016,7 @@ public class AlignFrame extends Frame alignPanel.repaint(); } - public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void selectAllSequenceMenuItem_actionPerformed() { SequenceGroup sg = new SequenceGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) @@ -643,17 +1029,23 @@ public class AlignFrame extends Frame PaintRefresher.Refresh(null, viewport.alignment); } - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void deselectAllSequenceMenuItem_actionPerformed() { + if(viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1=null; + alignPanel.seqPanel.keyboardNo2=null; + } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); + alignPanel.idPanel.idCanvas.searchResults = null; alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } - public void invertSequenceMenuItem_actionPerformed(ActionEvent e) + public void invertSequenceMenuItem_actionPerformed() { SequenceGroup sg = viewport.getSelectionGroup(); for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++) @@ -664,17 +1056,18 @@ public class AlignFrame extends Frame PaintRefresher.Refresh(null, viewport.alignment); } - public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + public void remove2LeftMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) { - addHistoryItem(new HistoryItem("Remove Left", viewport.alignment, + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Left", viewport.alignment, HistoryItem.HIDE)); int min = colSel.getMin(); viewport.getAlignment().trimLeft(min); colSel.compensateForEdit(0, min); - + edit.addShift(0, min); if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveLeft(min); @@ -693,7 +1086,7 @@ public class AlignFrame extends Frame } } - public void remove2RightMenuItem_actionPerformed(ActionEvent e) + public void remove2RightMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) @@ -702,6 +1095,7 @@ public class AlignFrame extends Frame HistoryItem.HIDE)); int max = colSel.getMax(); viewport.getAlignment().trimRight(max); + if (viewport.getSelectionGroup() != null) { viewport.getSelectionGroup().adjustForRemoveRight(max); @@ -721,9 +1115,10 @@ public class AlignFrame extends Frame } - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + public void removeGappedColumnMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gapped Columns", + HistoryItem edit; + addHistoryItem(edit=new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); @@ -739,9 +1134,12 @@ public class AlignFrame extends Frame viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + public void removeAllGapsMenuItem_actionPerformed() { - addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, + // TODO: hidden regions should not be touched by removeAllGaps - a minimal number of gaps will remain in alignment segments containing uneven length subsequences + // TODO: columnSelection.compensateforedits should be called (and passed to history item) + HistoryItem editgaps; + addHistoryItem(editgaps=new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); //This is to maintain viewport position on first residue @@ -750,79 +1148,75 @@ public class AlignFrame extends Frame int startRes = seq.findPosition(viewport.startRes); SequenceI current; - int jSize; - Vector seqs=null; int start=0, end = viewport.alignment.getWidth(); if (viewport.getSelectionGroup() != null - && viewport.getSelectionGroup().sequences != null - && viewport.getSelectionGroup().sequences.size()>0) + && viewport.getSelectionGroup().getSequences(false) != null + && viewport.getSelectionGroup().getSize(false)>0) { - seqs = viewport.getSelectionGroup().sequences; + seqs = viewport.getSelectionGroup().getSequences(true); start = viewport.getSelectionGroup().getStartRes(); end = viewport.getSelectionGroup().getEndRes()+1; } else seqs = viewport.alignment.getSequences(); + /* Commented out regions below are partial implementation of todo above. + * divide start,end into visible chunks, and for each: + int diff=end-start+1; + int diffmax=0; + int dr[] = new int[seqs.size()]; + */ for (int i = 0; i < seqs.size(); i++) { current = (SequenceI) seqs.elementAt(i); - jSize = current.getLength(); - - // Removing a range is much quicker than removing gaps - // one by one for long sequences - int j = start; - int rangeStart=-1, rangeEnd=-1; - - 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); - } + //dr[i]= + current.removeGaps(start, end); + /*if (d0) { + // record shift for history. + editgaps.addShift(start, diff); + if (viewport.hasHiddenColumns && diffmax>diff) { + // pad sequence + StringBuffer gaps=new StringBuffer(diffmax); + for (int i=0,j=diffmax-diff; i0) { + String sq = current.getSequence(); + current.setSequence(sq.substring(0, hcend-dr[i])+gaps.substring(0, dr[i]-diff)+sq.substring()); + } + } + } + }*/ + viewport.setStartRes(seq.findIndex(startRes)-1); viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void alignmentChanged() { - viewport.updateConsensus(); - viewport.updateConservation (); + viewport.alignment.padGaps(); + if(viewport.autocalculateConsensus) + { + viewport.updateConsensus(); + viewport.updateConservation(); + } + resetAllColourSchemes(); if(alignPanel.overviewPanel!=null) alignPanel.overviewPanel.updateOverviewImage(); + + viewport.alignment.adjustSequenceAnnotations(); alignPanel.repaint(); } @@ -859,7 +1253,8 @@ public class AlignFrame extends Frame SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s); if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme) { - ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth()); + ((ClustalxColourScheme)sg.cs).resetClustalX( + sg.getSequences(true), sg.getWidth()); } sg.recalcConservation(); } @@ -867,18 +1262,18 @@ public class AlignFrame extends Frame - public void findMenuItem_actionPerformed(ActionEvent e) + public void findMenuItem_actionPerformed() { new Finder(alignPanel); } - public void font_actionPerformed(ActionEvent e) + public void font_actionPerformed() { new FontChooser(alignPanel); } - public void seqLimits_itemStateChanged(ItemEvent e) + public void seqLimits_itemStateChanged() { viewport.setShowJVSuffix(seqLimits.getState()); alignPanel.fontChanged(); @@ -886,13 +1281,13 @@ public class AlignFrame extends Frame } - protected void colourTextMenuItem_actionPerformed(ActionEvent e) + protected void colourTextMenuItem_actionPerformed() { viewport.setColourText(colourTextMenuItem.getState()); alignPanel.repaint(); } - protected void wrapMenuItem_actionPerformed(ActionEvent e) + protected void wrapMenuItem_actionPerformed() { viewport.setWrapAlignment(wrapMenuItem.getState()); alignPanel.setWrapAlignment(wrapMenuItem.getState()); @@ -902,49 +1297,55 @@ public class AlignFrame extends Frame alignPanel.repaint(); } - protected void scaleAbove_actionPerformed(ActionEvent e) + + protected void scaleAbove_actionPerformed() { viewport.setScaleAboveWrapped(scaleAbove.getState()); alignPanel.repaint(); } - protected void scaleLeft_actionPerformed(ActionEvent e) + protected void scaleLeft_actionPerformed() { viewport.setScaleLeftWrapped(scaleLeft.getState()); alignPanel.repaint(); } - protected void scaleRight_actionPerformed(ActionEvent e) + protected void scaleRight_actionPerformed() { viewport.setScaleRightWrapped(scaleRight.getState()); alignPanel.repaint(); } - public void viewBoxesMenuItem_actionPerformed(ActionEvent e) + public void viewBoxesMenuItem_actionPerformed() { viewport.setShowBoxes(viewBoxesMenuItem.getState()); alignPanel.repaint(); } - public void viewTextMenuItem_actionPerformed(ActionEvent e) + public void viewTextMenuItem_actionPerformed() { viewport.setShowText(viewTextMenuItem.getState()); alignPanel.repaint(); } - protected void renderGapsMenuItem_actionPerformed(ActionEvent e) + protected void renderGapsMenuItem_actionPerformed() { viewport.setRenderGaps(renderGapsMenuItem.getState()); alignPanel.repaint(); } - public void annotationPanelMenuItem_actionPerformed(ActionEvent e) + public void annotationPanelMenuItem_actionPerformed() { viewport.setShowAnnotation(annotationPanelMenuItem.getState()); alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState()); } - public void overviewMenuItem_actionPerformed(ActionEvent e) + public void featureSettings_actionPerformed() + { + new FeatureSettings(viewport, alignPanel); + } + + public void overviewMenuItem_actionPerformed() { if (alignPanel.overviewPanel != null) { @@ -972,59 +1373,59 @@ public class AlignFrame extends Frame } - protected void noColourmenuItem_actionPerformed(ActionEvent e) + protected void noColourmenuItem_actionPerformed() { changeColour(null); } - public void clustalColour_actionPerformed(ActionEvent e) + public void clustalColour_actionPerformed() { abovePIDThreshold.setState(false); changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(), viewport.alignment.getWidth())); } - public void zappoColour_actionPerformed(ActionEvent e) + public void zappoColour_actionPerformed() { changeColour(new ZappoColourScheme()); } - public void taylorColour_actionPerformed(ActionEvent e) + public void taylorColour_actionPerformed() { changeColour(new TaylorColourScheme()); } - public void hydrophobicityColour_actionPerformed(ActionEvent e) + public void hydrophobicityColour_actionPerformed() { changeColour(new HydrophobicColourScheme()); } - public void helixColour_actionPerformed(ActionEvent e) + public void helixColour_actionPerformed() { changeColour(new HelixColourScheme()); } - public void strandColour_actionPerformed(ActionEvent e) + public void strandColour_actionPerformed() { changeColour(new StrandColourScheme()); } - public void turnColour_actionPerformed(ActionEvent e) + public void turnColour_actionPerformed() { changeColour(new TurnColourScheme()); } - public void buriedColour_actionPerformed(ActionEvent e) + public void buriedColour_actionPerformed() { changeColour(new BuriedColourScheme()); } - public void nucleotideColour_actionPerformed(ActionEvent e) + public void nucleotideColour_actionPerformed() { changeColour(new NucleotideColourScheme()); } - protected void applyToAllGroups_actionPerformed(ActionEvent e) + protected void applyToAllGroups_actionPerformed() { viewport.setColourAppliesToAllGroups(applyToAllGroups.getState()); } @@ -1090,7 +1491,7 @@ public class AlignFrame extends Frame } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -1110,7 +1511,7 @@ public class AlignFrame extends Frame || 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(true), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1119,7 +1520,7 @@ public class AlignFrame extends Frame { Conservation c = new Conservation("Group", ResidueProperties.propHash, 3, - sg.sequences, 0, + sg.getSequences(true), 0, viewport.alignment.getWidth() - 1); c.calculate(); c.verdict(false, viewport.ConsPercGaps); @@ -1145,7 +1546,7 @@ public class AlignFrame extends Frame - protected void modifyPID_actionPerformed(ActionEvent e) + protected void modifyPID_actionPerformed() { if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null) { @@ -1155,7 +1556,7 @@ public class AlignFrame extends Frame } } - protected void modifyConservation_actionPerformed(ActionEvent e) + protected void modifyConservation_actionPerformed() { if (viewport.getConservationSelected() && viewport.globalColourScheme!=null) { @@ -1165,7 +1566,7 @@ public class AlignFrame extends Frame } } - protected void conservationMenuItem_actionPerformed(ActionEvent e) + protected void conservationMenuItem_actionPerformed() { viewport.setConservationSelected(conservationMenuItem.getState()); @@ -1174,10 +1575,10 @@ public class AlignFrame extends Frame changeColour(viewport.getGlobalColourScheme()); - modifyConservation_actionPerformed(null); + modifyConservation_actionPerformed(); } - public void abovePIDThreshold_actionPerformed(ActionEvent e) + public void abovePIDThreshold_actionPerformed() { viewport.setAbovePIDThreshold(abovePIDThreshold.getState()); @@ -1186,25 +1587,25 @@ public class AlignFrame extends Frame changeColour(viewport.getGlobalColourScheme()); - modifyPID_actionPerformed(null); + modifyPID_actionPerformed(); } - public void userDefinedColour_actionPerformed(ActionEvent e) + public void userDefinedColour_actionPerformed() { new UserDefinedColours(alignPanel, null); } - public void PIDColour_actionPerformed(ActionEvent e) + public void PIDColour_actionPerformed() { changeColour(new PIDColourScheme()); } - public void BLOSUM62Colour_actionPerformed(ActionEvent e) + public void BLOSUM62Colour_actionPerformed() { changeColour(new Blosum62ColourScheme()); } - public void sortPairwiseMenuItem_actionPerformed(ActionEvent e) + public void sortPairwiseMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment, HistoryItem.SORT)); @@ -1213,7 +1614,7 @@ public class AlignFrame extends Frame alignPanel.repaint(); } - public void sortIDMenuItem_actionPerformed(ActionEvent e) + public void sortIDMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("ID Sort", viewport.alignment, HistoryItem.SORT)); @@ -1221,7 +1622,7 @@ public class AlignFrame extends Frame alignPanel.repaint(); } - public void sortGroupMenuItem_actionPerformed(ActionEvent e) + public void sortGroupMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Group Sort", viewport.alignment, HistoryItem.SORT)); @@ -1230,19 +1631,15 @@ public class AlignFrame extends Frame } - public void removeRedundancyMenuItem_actionPerformed(ActionEvent e) + 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(ActionEvent e) + public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup()!=null + && viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1250,7 +1647,7 @@ public class AlignFrame extends Frame } } - public void PCAMenuItem_actionPerformed(ActionEvent e) + public void PCAMenuItem_actionPerformed() { //are the sequences aligned? if (!viewport.alignment.isAligned()) @@ -1272,8 +1669,8 @@ public class AlignFrame extends Frame } if ( (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() < 4 && - viewport.getSelectionGroup().getSize() > 0) + viewport.getSelectionGroup().getSize(false) < 4 && + viewport.getSelectionGroup().getSize(false) > 0) || viewport.getAlignment().getHeight() < 4) { return; @@ -1289,22 +1686,22 @@ public class AlignFrame extends Frame } - public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e) + public void averageDistanceTreeMenuItem_actionPerformed() { NewTreePanel("AV", "PID", "Average distance tree using PID"); } - public void neighbourTreeMenuItem_actionPerformed(ActionEvent e) + public void neighbourTreeMenuItem_actionPerformed() { NewTreePanel("NJ", "PID", "Neighbour joining tree using PID"); } - protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void njTreeBlosumMenuItem_actionPerformed() { NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62"); } - protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e) + protected void avTreeBlosumMenuItem_actionPerformed() { NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID"); } @@ -1331,23 +1728,39 @@ public class AlignFrame extends Frame } - 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(false) > 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.treeImport = true; + 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); } void addTreeMenuItem(final TreePanel treePanel, String title) @@ -1356,7 +1769,7 @@ public class AlignFrame extends Frame sortByTreeMenu.add(item); item.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) + public void actionPerformed(ActionEvent evt) { addHistoryItem(new HistoryItem("Sort", viewport.alignment, HistoryItem.SORT)); @@ -1374,12 +1787,12 @@ public class AlignFrame extends Frame }); } - protected void documentation_actionPerformed(ActionEvent e) + protected void documentation_actionPerformed() { - showURL("http://www.jalview.org/help.html"); + showURL("http://www.jalview.org/help.html", "HELP"); } - protected void about_actionPerformed(ActionEvent e) + protected void about_actionPerformed() { class AboutPanel extends Canvas @@ -1410,7 +1823,7 @@ public class AlignFrame extends Frame 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); } } @@ -1444,20 +1857,9 @@ public class AlignFrame extends Frame } - /** - * Displays the given URL in a new browser window - * - * @param url URL to display in browser window. - *
New window will be named "HELP_WINDOW" - */ - public void showURL(String url) - { - showURL(url, "HELP"); - } - public void showURL(String url, String target) { - if (applet == null) + if (viewport.applet == null) { System.out.println("Not running as applet - no browser available."); } @@ -1465,7 +1867,8 @@ public class AlignFrame extends Frame { 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) @@ -1480,15 +1883,17 @@ public class AlignFrame extends Frame //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 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(); @@ -1536,7 +1941,7 @@ public class AlignFrame extends Frame MenuItem delete = new MenuItem(); MenuItem copy = new MenuItem(); MenuItem cut = new MenuItem(); - Menu Menu1 = new Menu(); + Menu pasteMenu = new Menu(); MenuItem pasteNew = new MenuItem(); MenuItem pasteThis = new MenuItem(); protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); @@ -1546,6 +1951,8 @@ public class AlignFrame extends Frame 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(); @@ -1554,20 +1961,28 @@ public class AlignFrame extends Frame MenuItem documentation = new MenuItem(); MenuItem about = new MenuItem(); protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); - - private void jbInit() throws Exception { + Panel embeddedMenu; + Label embeddedEdit; + Label embeddedSearch; + Label embeddedView; + Label embeddedColour; + Label embeddedFile; + Label embeddedHelp; + Label embeddedCalculate; + FlowLayout flowLayout1; + + private void jbInit() throws Exception { setMenuBar(alignFrameMenuBar); 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) @@ -1578,124 +1993,44 @@ public class AlignFrame extends Frame outputTextboxMenu.add(item); } + closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); - - fileMenu.setLabel("File"); - closeMenuItem.setLabel("Close"); - closeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - closeMenuItem_actionPerformed(e); - } - }); - editMenu.setLabel("Edit"); - viewMenu.setLabel("View"); - colourMenu.setLabel("Colour"); - calculateMenu.setLabel("Calculate"); - selectAllSequenceMenuItem.setLabel("Select all"); - selectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - selectAllSequenceMenuItem_actionPerformed(e); - } - }); - deselectAllSequenceMenuItem.setLabel("Deselect All"); - deselectAllSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - deselectAllSequenceMenuItem_actionPerformed(e); - } - }); - invertSequenceMenuItem.setLabel("Invert Selection"); - invertSequenceMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - invertSequenceMenuItem_actionPerformed(e); - } - }); + loadTree.addActionListener(this); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.addActionListener(this); remove2LeftMenuItem.setLabel("Remove Left"); - remove2LeftMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - remove2LeftMenuItem_actionPerformed(e); - } - }); + remove2LeftMenuItem.addActionListener(this); remove2RightMenuItem.setLabel("Remove Right"); - remove2RightMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - remove2RightMenuItem_actionPerformed(e); - } - }); + remove2RightMenuItem.addActionListener(this); removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); - removeGappedColumnMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeGappedColumnMenuItem_actionPerformed(e); - } - }); + removeGappedColumnMenuItem.addActionListener(this); removeAllGapsMenuItem.setLabel("Remove All Gaps"); - removeAllGapsMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeAllGapsMenuItem_actionPerformed(e); - } - }); + removeAllGapsMenuItem.addActionListener(this); viewBoxesMenuItem.setLabel("Boxes"); viewBoxesMenuItem.setState(true); - viewBoxesMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - viewBoxesMenuItem_actionPerformed(null); - } - }); + viewBoxesMenuItem.addItemListener(this); viewTextMenuItem.setLabel("Text"); viewTextMenuItem.setState(true); - viewTextMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - viewTextMenuItem_actionPerformed(null); - } - }); + viewTextMenuItem.addItemListener(this); sortPairwiseMenuItem.setLabel("by Pairwise Identity"); - sortPairwiseMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortPairwiseMenuItem_actionPerformed(e); - } - }); + sortPairwiseMenuItem.addActionListener(this); sortIDMenuItem.setLabel("by ID"); - sortIDMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortIDMenuItem_actionPerformed(e); - } - }); + sortIDMenuItem.addActionListener(this); sortGroupMenuItem.setLabel("by Group"); - sortGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - sortGroupMenuItem_actionPerformed(e); - } - }); + sortGroupMenuItem.addActionListener(this); removeRedundancyMenuItem.setLabel("Remove Redundancy..."); - removeRedundancyMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - removeRedundancyMenuItem_actionPerformed(e); - } - }); + removeRedundancyMenuItem.addActionListener(this); pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); - pairwiseAlignmentMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pairwiseAlignmentMenuItem_actionPerformed(e); - } - }); + pairwiseAlignmentMenuItem.addActionListener(this); PCAMenuItem.setLabel("Principal Component Analysis"); - PCAMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - PCAMenuItem_actionPerformed(e); - } - }); + PCAMenuItem.addActionListener(this); averageDistanceTreeMenuItem.setLabel( "Average Distance Using % Identity"); - averageDistanceTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - averageDistanceTreeMenuItem_actionPerformed(e); - } - }); + averageDistanceTreeMenuItem.addActionListener(this); neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); - neighbourTreeMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - neighbourTreeMenuItem_actionPerformed(e); - } - }); + 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)); @@ -1703,281 +2038,132 @@ public class AlignFrame extends Frame outputTextboxMenu.setLabel("Output to Textbox"); clustalColour.setLabel("Clustalx"); - clustalColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - clustalColour_actionPerformed(e); - } - }); + clustalColour.addActionListener(this); zappoColour.setLabel("Zappo"); - zappoColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - zappoColour_actionPerformed(e); - } - }); + zappoColour.addActionListener(this); taylorColour.setLabel("Taylor"); - taylorColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - taylorColour_actionPerformed(e); - } - }); + taylorColour.addActionListener(this); hydrophobicityColour.setLabel("Hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - hydrophobicityColour_actionPerformed(e); - } - }); + hydrophobicityColour.addActionListener(this); helixColour.setLabel("Helix Propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - helixColour_actionPerformed(e); - } - }); + helixColour.addActionListener(this); strandColour.setLabel("Strand Propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - strandColour_actionPerformed(e); - } - }); + strandColour.addActionListener(this); turnColour.setLabel("Turn Propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - turnColour_actionPerformed(e); - } - }); + turnColour.addActionListener(this); buriedColour.setLabel("Buried Index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - buriedColour_actionPerformed(e); - } - }); + buriedColour.addActionListener(this); userDefinedColour.setLabel("User Defined..."); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - userDefinedColour_actionPerformed(e); - } - }); + userDefinedColour.addActionListener(this); PIDColour.setLabel("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - PIDColour_actionPerformed(e); - } - }); + PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62 Score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - BLOSUM62Colour_actionPerformed(e); - } - }); + BLOSUM62Colour.addActionListener(this); avDistanceTreeBlosumMenuItem.setLabel( "Average Distance Using BLOSUM62"); - avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - avTreeBlosumMenuItem_actionPerformed(e); - } - }); + avDistanceTreeBlosumMenuItem.addActionListener(this); njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); - njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - njTreeBlosumMenuItem_actionPerformed(e); - } - }); - annotationPanelMenuItem.setActionCommand(""); - annotationPanelMenuItem.setState(true); + njTreeBlosumMenuItem.addActionListener(this); annotationPanelMenuItem.setLabel("Show Annotations"); - annotationPanelMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - annotationPanelMenuItem_actionPerformed(null); - } - }); + annotationPanelMenuItem.addItemListener(this); colourTextMenuItem.setLabel("Colour Text"); - colourTextMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - colourTextMenuItem_actionPerformed(null); - } - }); + colourTextMenuItem.addItemListener(this); overviewMenuItem.setLabel("Overview Window"); - overviewMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - overviewMenuItem_actionPerformed(e); - } - }); + overviewMenuItem.addActionListener(this); undoMenuItem.setEnabled(false); undoMenuItem.setLabel("Undo"); - undoMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - undoMenuItem_actionPerformed(e); - } - }); + undoMenuItem.addActionListener(this); redoMenuItem.setEnabled(false); redoMenuItem.setLabel("Redo"); - redoMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - redoMenuItem_actionPerformed(e); - } - }); + redoMenuItem.addActionListener(this); conservationMenuItem.setLabel("by Conservation"); - conservationMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - conservationMenuItem_actionPerformed(null); - } - }); + conservationMenuItem.addItemListener(this); noColourmenuItem.setLabel("None"); - noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - noColourmenuItem_actionPerformed(e); - } - }); + noColourmenuItem.addActionListener(this); wrapMenuItem.setLabel("Wrap"); - wrapMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - wrapMenuItem_actionPerformed(null); - } - }); + wrapMenuItem.addItemListener(this); renderGapsMenuItem.setLabel("Show Gaps"); renderGapsMenuItem.setState(true); - renderGapsMenuItem.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - renderGapsMenuItem_actionPerformed(null); - } - }); + renderGapsMenuItem.addItemListener(this); findMenuItem.setLabel("Find..."); - findMenuItem.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - findMenuItem_actionPerformed(e); - } - }); + findMenuItem.addActionListener(this); searchMenu.setLabel("Search"); abovePIDThreshold.setLabel("Above Identity Threshold"); - abovePIDThreshold.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - abovePIDThreshold_actionPerformed(null); - } - }); + abovePIDThreshold.addItemListener(this); nucleotideColour.setLabel("Nucleotide"); - nucleotideColour.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - nucleotideColour_actionPerformed(e); - } - }); + nucleotideColour.addActionListener(this); deleteGroups.setLabel("Undefine Groups"); - deleteGroups.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - deleteGroups_actionPerformed(e); - } - }); + deleteGroups.addActionListener(this); copy.setLabel("Copy"); - copy.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - copy_actionPerformed(e); - } - }); + copy.addActionListener(this); cut.setLabel("Cut"); - cut.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - cut_actionPerformed(e); - } - }); + cut.addActionListener(this); delete.setLabel("Delete"); - delete.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - delete_actionPerformed(e); - } - }); - Menu1.setLabel("Paste"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); pasteNew.setLabel("To New Alignment"); - pasteNew.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pasteNew_actionPerformed(e); - } - }); + pasteNew.addActionListener(this); pasteThis.setLabel("Add To This Alignment"); - pasteThis.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - pasteThis_actionPerformed(e); - } - }); + pasteThis.addActionListener(this); applyToAllGroups.setLabel("Apply Colour To All Groups"); applyToAllGroups.setState(true); - applyToAllGroups.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - applyToAllGroups_actionPerformed(null); - } - }); + applyToAllGroups.addItemListener(this); font.setLabel("Font..."); - font.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - font_actionPerformed(e); - } - }); + font.addActionListener(this); scaleAbove.setLabel("Scale Above"); scaleAbove.setState(true); - scaleAbove.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleAbove_actionPerformed(null); - } - }); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); scaleLeft.setEnabled(false); scaleLeft.setState(true); scaleLeft.setLabel("Scale Left"); - scaleLeft.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleLeft_actionPerformed(null); - } - }); + scaleLeft.addItemListener(this); scaleRight.setEnabled(false); scaleRight.setState(true); scaleRight.setLabel("Scale Right"); - scaleRight.addItemListener(new java.awt.event.ItemListener() { - public void itemStateChanged(ItemEvent e) { - scaleRight_actionPerformed(null); - } - }); + scaleRight.addItemListener(this); modifyPID.setLabel("Modify Identity Threshold..."); - modifyPID.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - modifyPID_actionPerformed(e); - } - }); + modifyPID.addActionListener(this); modifyConservation.setLabel("Modify Conservation Threshold..."); - modifyConservation.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - modifyConservation_actionPerformed(e); - } - }); + 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(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - inputText_actionPerformed(e); - } - }); + inputText.addActionListener(this); helpMenu.setLabel("Help"); documentation.setLabel("Documentation"); - documentation.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - documentation_actionPerformed(e); - } - }); + documentation.addActionListener(this); about.setLabel("About..."); - about.addActionListener(new java.awt.event.ActionListener() { - public void actionPerformed(ActionEvent e) { - about_actionPerformed(e); - } - }); + about.addActionListener(this); seqLimits.setState(true); seqLimits.setLabel("Show Sequence Limits"); - seqLimits.addItemListener(new ItemListener() - { - public void itemStateChanged(ItemEvent e) - { - seqLimits_itemStateChanged(e); - } - }); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + featureSettings.addActionListener(this); + sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.addItemListener(this); + 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); + alignFrameMenuBar.add(fileMenu); alignFrameMenuBar.add(editMenu); @@ -1988,19 +2174,23 @@ public class AlignFrame extends Frame 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(Menu1); + editMenu.add(pasteMenu); editMenu.add(delete); editMenu.addSeparator(); editMenu.add(selectAllSequenceMenuItem); editMenu.add(deselectAllSequenceMenuItem); editMenu.add(invertSequenceMenuItem); - editMenu.add(deleteGroups); + editMenu.add(invertColSel); + editMenu.add(deleteGroups); editMenu.addSeparator(); editMenu.add(remove2LeftMenuItem); editMenu.add(remove2RightMenuItem); @@ -2010,19 +2200,24 @@ public class AlignFrame extends Frame searchMenu.add(findMenuItem); viewMenu.add(font); viewMenu.addSeparator(); - viewMenu.add(seqLimits); - viewMenu.addSeparator(); + viewMenu.add(menu1); + viewMenu.add(menu2); + viewMenu.addSeparator(); viewMenu.add(wrapMenuItem); viewMenu.add(scaleAbove); viewMenu.add(scaleLeft); viewMenu.add(scaleRight); viewMenu.addSeparator(); + viewMenu.add(seqLimits); viewMenu.add(viewBoxesMenuItem); viewMenu.add(viewTextMenuItem); viewMenu.add(colourTextMenuItem); viewMenu.add(renderGapsMenuItem); viewMenu.add(annotationPanelMenuItem); - viewMenu.addSeparator(); + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + viewMenu.addSeparator(); viewMenu.add(overviewMenuItem); colourMenu.add(applyToAllGroups); colourMenu.addSeparator(); @@ -2044,14 +2239,16 @@ public class AlignFrame extends Frame 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); - Menu1.add(pasteNew); - Menu1.add(pasteThis); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); sort.add(sortIDMenuItem); sort.add(sortByTreeMenu); sort.add(sortGroupMenuItem); @@ -2062,6 +2259,154 @@ public class AlignFrame extends Frame calculate.add(njTreeBlosumMenuItem); helpMenu.add(documentation); helpMenu.add(about); + menu1.add(showColumns); + menu1.add(showSeqs); + menu2.add(hideColumns); + menu2.add(hideSequences); + } + + 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(); + 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"); + embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10)); + embeddedColour.setText("Colour"); + 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(embeddedView); + embeddedMenu.add(embeddedColour); + embeddedMenu.add(embeddedCalculate); + embeddedMenu.add(embeddedHelp); + flowLayout1.setAlignment(FlowLayout.LEFT); + flowLayout1.setHgap(2); + flowLayout1.setVgap(0); + embeddedFile.addMouseListener(this); + embeddedEdit.addMouseListener(this); + embeddedSearch.addMouseListener(this); + embeddedView.addMouseListener(this); + embeddedColour.addMouseListener(this); + 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 + - embeddedMenu.HEIGHT - statusBar.HEIGHT); + + viewport.applet.add(alignPanel, BorderLayout.CENTER); + viewport.applet.validate(); + + } + + + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, 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(); + + public void mousePressed(MouseEvent evt) + { + PopupMenu popup = null; + Label source = (Label)evt.getSource(); + if(source==embeddedFile) + { + popup = filePopup = genPopupMenu(filePopup, fileMenu); + } + else if(source==embeddedEdit) + { + popup = editPopup = genPopupMenu(editPopup, editMenu); + } + else if(source==embeddedSearch) + { + popup = searchPopup = genPopupMenu(searchPopup, searchMenu); + } + else if(source==embeddedView) + { + popup = viewPopup = genPopupMenu(viewPopup, viewMenu); } + else if(source==embeddedColour) + { + popup = colourPopup = genPopupMenu(colourPopup, colourMenu); + } + else if(source==embeddedCalculate) + { + popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu); + } + else if(source==embeddedHelp) + { + popup = helpPopup = genPopupMenu(helpPopup, helpMenu); + } + + embeddedMenu.add(popup); + popup.show(embeddedMenu, + source.getBounds().x, + source.getBounds().y + source.getBounds().getSize().height); + } + + PopupMenu genPopupMenu(PopupMenu popup, Menu original) + { + if(popup!=null) + { + return popup; + } + popup = new PopupMenu(); + int m, mSize = original.getItemCount(); + for(m=0; m