X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=01bea4d2ca495a78d649b46ceea508837daecc2b;hb=d355ad106f73e0de0abc3fb3f375af4eaf352591;hp=613825747cda7cb262627c66f0aea9b87065c034;hpb=95a46891288f4fc63d690cab4f56879678f54fb6;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 6138257..01bea4d 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -19,7 +19,6 @@ package jalview.appletgui; -import jalview.jbappletgui.GAlignFrame; import jalview.schemes.*; import jalview.datamodel.*; import jalview.analysis.*; @@ -29,65 +28,397 @@ import java.awt.event.*; import java.util.*; import java.io.InputStreamReader; import java.io.BufferedReader; +import java.net.URL; -public class AlignFrame - extends GAlignFrame + +public class AlignFrame extends Frame implements ActionListener, + ItemListener, KeyListener, MouseListener { - final AlignmentPanel alignPanel; - final AlignViewport viewport; - public static final int NEW_WINDOW_WIDTH = 700; - public static final int NEW_WINDOW_HEIGHT = 500; + public AlignmentPanel alignPanel; + public AlignViewport viewport; + int NEW_WINDOW_WIDTH = 700; + int NEW_WINDOW_HEIGHT = 500; jalview.bin.JalviewLite applet; - public AlignFrame(AlignmentI al) - { - this.applet = null; - viewport = new AlignViewport(al, null); - alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - } - public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet) + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title) { + try{ + jbInit(); + }catch(Exception ex) + { + ex.printStackTrace(); + } + this.applet = applet; viewport = new AlignViewport(al, applet); alignPanel = new AlignmentPanel(this, viewport); - add(alignPanel); - alignPanel.validate(); - String treeFile = applet.getParameter("treeFile"); - TreePanel treepanel = null; - if (treeFile != null) + annotationPanelMenuItem.setState(viewport.showAnnotation); + + if(applet!=null) { - try + String param = applet.getParameter("sortBy"); + if (param != null) { - treeFile = treeFile; - jalview.io.NewickFile fin = new jalview.io.NewickFile(applet. - getCodeBase() + treeFile, "URL"); - fin.parse(); + if (param.equalsIgnoreCase("Id")) + sortIDMenuItem_actionPerformed(); + else if (param.equalsIgnoreCase("Pairwise Identity")) + sortPairwiseMenuItem_actionPerformed(); + } - if (fin.getTree() != null) + param = applet.getParameter("wrap"); + if (param != null) + { + if (param.equalsIgnoreCase("true")) { - 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); + wrapMenuItem.setState(true); + wrapMenuItem_actionPerformed(); } } - catch (Exception ex) + + try { - ex.printStackTrace(); + param = applet.getParameter("windowWidth"); + if (param != null) + { + int width = Integer.parseInt(param); + NEW_WINDOW_WIDTH = width; + } + param = applet.getParameter("windowHeight"); + if (param != null) + { + int height = Integer.parseInt(param); + NEW_WINDOW_HEIGHT = height; + } } + catch (Exception ex) + {} + } + //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); + + 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.validate(); + alignPanel.repaint(); + } + public AlignViewport getAlignViewport() + { + return viewport; + } + public SeqCanvas getSeqcanvas() + { + return alignPanel.seqPanel.seqCanvas; } - public void inputText_actionPerformed(ActionEvent e) + + /** + * DOCUMENT ME! + * + * @param String DOCUMENT ME! + */ + + public void parseFeaturesFile(String file) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(true); + try + { + 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); + } + } + + viewport.showSequenceFeatures = true; + viewMenu.addSeparator(); + viewMenu.add(sequenceFeatures); + viewMenu.add(featureSettings); + + + alignPanel.repaint(); + + } + catch (Exception ex) + { + ex.printStackTrace(); + System.out.println("Error parsing groups file: " + ex); + } + } + + public void keyPressed(KeyEvent evt) + { + switch (evt.getKeyCode()) + { + case 27: // escape key + deselectAllSequenceMenuItem_actionPerformed(); + break; + case KeyEvent.VK_X: + if (evt.isControlDown() || evt.isMetaDown()) + { + cut_actionPerformed(); + } + break; + case KeyEvent.VK_C: + 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: + moveSelectedSequences(false); + break; + case KeyEvent.VK_UP: + moveSelectedSequences(true); + break; + case KeyEvent.VK_F: + if (evt.isControlDown()) + { + findMenuItem_actionPerformed(); + } + break; + case KeyEvent.VK_BACK_SPACE: + case KeyEvent.VK_DELETE: + cut_actionPerformed(); + break; + } + } + 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(); + } + public void actionPerformed(ActionEvent evt) + { + if(evt.getSource()==inputText) + inputText_actionPerformed(); + else if(evt.getSource()==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(evt.getSource()==copy) + copy_actionPerformed(); + else if(evt.getSource()==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(evt.getSource()==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(evt.getSource()==inputText) + inputText_actionPerformed(); + else if(evt.getSource()==closeMenuItem) + closeMenuItem_actionPerformed(); + else if(evt.getSource()==undoMenuItem) + undoMenuItem_actionPerformed(); + else if(evt.getSource()==redoMenuItem) + redoMenuItem_actionPerformed(); + else if(evt.getSource()==copy) + copy_actionPerformed(); + else if(evt.getSource()==pasteNew) + pasteNew_actionPerformed(); + else if(evt.getSource()==pasteThis) + pasteThis_actionPerformed(); + else if(evt.getSource()==cut) + cut_actionPerformed(); + else if(evt.getSource()==delete) + delete_actionPerformed(); + else if(evt.getSource()==deleteGroups) + deleteGroups_actionPerformed(); + else if(evt.getSource()==selectAllSequenceMenuItem) + selectAllSequenceMenuItem_actionPerformed(); + else if(evt.getSource()==deselectAllSequenceMenuItem) + deselectAllSequenceMenuItem_actionPerformed(); + else if(evt.getSource()==invertSequenceMenuItem) + invertSequenceMenuItem_actionPerformed(); + else if(evt.getSource()==remove2LeftMenuItem) + remove2LeftMenuItem_actionPerformed(); + else if(evt.getSource()==remove2RightMenuItem) + remove2RightMenuItem_actionPerformed(); + else if(evt.getSource()==removeGappedColumnMenuItem) + removeGappedColumnMenuItem_actionPerformed(); + else if(evt.getSource()==removeAllGapsMenuItem) + removeAllGapsMenuItem_actionPerformed(); + else if(evt.getSource()==findMenuItem) + findMenuItem_actionPerformed(); + else if(evt.getSource()==font) + font_actionPerformed(); + else if(evt.getSource()==featureSettings) + featureSettings_actionPerformed(); + else if(evt.getSource()==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) + modifyPID_actionPerformed(); + else if(evt.getSource()==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) + sortPairwiseMenuItem_actionPerformed(); + else if(evt.getSource()==sortIDMenuItem) + sortIDMenuItem_actionPerformed(); + else if(evt.getSource()==sortGroupMenuItem) + sortGroupMenuItem_actionPerformed(); + else if(evt.getSource()==removeRedundancyMenuItem) + removeRedundancyMenuItem_actionPerformed(); + else if(evt.getSource()==pairwiseAlignmentMenuItem) + pairwiseAlignmentMenuItem_actionPerformed(); + else if(evt.getSource()==PCAMenuItem) + PCAMenuItem_actionPerformed(); + else if(evt.getSource()==averageDistanceTreeMenuItem) + averageDistanceTreeMenuItem_actionPerformed(); + else if(evt.getSource()==neighbourTreeMenuItem) + neighbourTreeMenuItem_actionPerformed(); + else if(evt.getSource()==njTreeBlosumMenuItem) + njTreeBlosumMenuItem_actionPerformed(); + else if(evt.getSource()==avDistanceTreeBlosumMenuItem) + avTreeBlosumMenuItem_actionPerformed(); + else if(evt.getSource()==documentation) + documentation_actionPerformed(); + else if(evt.getSource()==about) + about_actionPerformed(); + + } + + public void inputText_actionPerformed() + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500); @@ -95,20 +426,24 @@ public class AlignFrame protected void outputText_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); + CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet); Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, "Alignment output - " + e.getActionCommand(), 600, 500); - cap.setText(FormatAdapter.formatSequences(e.getActionCommand(), - viewport.getAlignment(). - getSequences())); + cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(), + viewport.getAlignment().getSequences(), + viewport.showJVSuffix)); } - public void closeMenuItem_actionPerformed(ActionEvent e) + public void closeMenuItem_actionPerformed() { - dispose(); + PaintRefresher.components.remove(viewport.alignment); + if(PaintRefresher.components.size()==0 && applet==null) + System.exit(0); + + this.dispose(); } Stack historyList = new Stack(); @@ -147,22 +482,21 @@ public class AlignFrame 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.HIDE)); restoreHistoryItem(hi); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - protected void redoMenuItem_actionPerformed(ActionEvent e) + protected void redoMenuItem_actionPerformed() { HistoryItem hi = (HistoryItem) redoList.pop(); restoreHistoryItem(hi); updateEditMenuBar(); - viewport.updateConsensus(); - alignPanel.repaint(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } // used by undo and redo @@ -206,9 +540,7 @@ public class AlignFrame updateEditMenuBar(); - viewport.updateConsensus(); - viewport.updateConservation(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } public void moveSelectedSequences(boolean up) @@ -264,7 +596,7 @@ public class AlignFrame } StringBuffer copiedSequences; - protected void copy_actionPerformed(ActionEvent e) + protected void copy_actionPerformed() { if (viewport.getSelectionGroup() == null) { @@ -334,12 +666,12 @@ public class AlignFrame } - 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)); @@ -382,7 +714,6 @@ public class AlignFrame newSeqs[i] = (SequenceI) seqs.elementAt(i); } - AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet); String newtitle = new String("Copied sequences"); if (getTitle().startsWith("Copied sequences")) { @@ -392,6 +723,8 @@ public class AlignFrame { newtitle = newtitle.concat("- from " + getTitle()); } + AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle); + jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH, NEW_WINDOW_HEIGHT); } @@ -399,9 +732,7 @@ public class AlignFrame { viewport.setEndSeq(viewport.alignment.getHeight()); viewport.alignment.getWidth(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } @@ -410,13 +741,13 @@ public class AlignFrame } - 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)); @@ -467,13 +798,11 @@ public class AlignFrame catch (Exception ex) {} } - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - protected void deleteGroups_actionPerformed(ActionEvent e) + protected void deleteGroups_actionPerformed() { viewport.alignment.deleteAllGroups(); viewport.setSelectionGroup(null); @@ -481,28 +810,31 @@ public class AlignFrame 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++) { sg.addSequence(viewport.getAlignment().getSequenceAt(i), false); } - sg.setEndRes(viewport.alignment.getWidth()); + sg.setEndRes(viewport.alignment.getWidth()-1); viewport.setSelectionGroup(sg); alignPanel.repaint(); PaintRefresher.Refresh(null, viewport.alignment); } - public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e) + public void deselectAllSequenceMenuItem_actionPerformed() { 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++) @@ -513,7 +845,7 @@ public class AlignFrame PaintRefresher.Refresh(null, viewport.alignment); } - public void remove2LeftMenuItem_actionPerformed(ActionEvent e) + public void remove2LeftMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) @@ -538,12 +870,11 @@ public class AlignFrame viewport.alignment.deleteGroup(sg); } } - - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } - public void remove2RightMenuItem_actionPerformed(ActionEvent e) + public void remove2RightMenuItem_actionPerformed() { ColumnSelection colSel = viewport.getColumnSelection(); if (colSel.size() > 0) @@ -566,28 +897,39 @@ public class AlignFrame viewport.alignment.deleteGroup(sg); } } - - alignPanel.repaint(); + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } } - public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e) + public void removeGappedColumnMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Remove Gapped Columns", viewport.alignment, HistoryItem.HIDE)); + + //This is to maintain viewport position on first residue + //of first sequence + SequenceI seq = viewport.alignment.getSequenceAt(0); + int startRes = seq.findPosition(viewport.startRes); + viewport.getAlignment().removeGaps(); - viewport.updateConservation(); - viewport.updateConsensus(); - alignPanel.repaint(); + + viewport.setStartRes(seq.findIndex(startRes)-1); + + viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences()); } - public void removeAllGapsMenuItem_actionPerformed(ActionEvent e) + public void removeAllGapsMenuItem_actionPerformed() { addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment, HistoryItem.HIDE)); + //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 current; int jSize; @@ -601,64 +943,139 @@ public class AlignFrame { seqs = viewport.getSelectionGroup().sequences; start = viewport.getSelectionGroup().getStartRes(); - end = viewport.getSelectionGroup().getEndRes(); + end = viewport.getSelectionGroup().getEndRes()+1; } else seqs = viewport.alignment.getSequences(); - for (int i = 0; i -1) + { + current.deleteChars(rangeStart, rangeEnd); + j-=rangeEnd-rangeStart; + jSize-=rangeEnd-rangeStart; + rangeStart = -1; + rangeEnd = -1; + } + else + j++; } - j++; } - while(j < end && j < jSize) ; + 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()); + } - viewport.updateConservation(); + public void alignmentChanged() + { viewport.updateConsensus(); + viewport.updateConservation (); + resetAllColourSchemes(); + if(alignPanel.overviewPanel!=null) + alignPanel.overviewPanel.updateOverviewImage(); + + viewport.alignment.adjustSequenceAnnotations(); alignPanel.repaint(); } - - public void findMenuItem_actionPerformed(ActionEvent e) + void resetAllColourSchemes() { - Finder finder = new Finder(alignPanel); + ColourSchemeI cs = viewport.globalColourScheme; + if(cs!=null) + { + 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); + } + } + + int s, sSize = viewport.alignment.getGroups().size(); + for(s=0; s 1) { Frame frame = new Frame(); - frame.add(new PairwiseAlignPanel(viewport)); + frame.add(new PairwiseAlignPanel(alignPanel)); jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500); } } - public void PCAMenuItem_actionPerformed(ActionEvent e) + public void PCAMenuItem_actionPerformed() { + //are the sequences aligned? + if (!viewport.alignment.isAligned()) + { + SequenceI current; + int Width = viewport.getAlignment().getWidth(); + + for (int i = 0; i < viewport.getAlignment().getSequences().size(); + i++) + { + current = viewport.getAlignment().getSequenceAt(i); + + if (current.getLength() < Width) + { + current.insertCharAt(Width - 1, viewport.getGapCharacter()); + } + } + alignPanel.repaint(); + } if ( (viewport.getSelectionGroup() != null && viewport.getSelectionGroup().getSize() < 4 && @@ -1042,11 +1469,7 @@ public class AlignFrame try { - PCAPanel pcaPanel = new PCAPanel(viewport, null); - Frame frame = new Frame(); - frame.add(pcaPanel); - jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis", - 400, 400); + new PCAPanel(viewport); } catch (java.lang.OutOfMemoryError ex) { @@ -1054,22 +1477,22 @@ public class AlignFrame } - 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"); } @@ -1115,13 +1538,13 @@ public class AlignFrame jalview.bin.JalviewLite.addFrame(tp, title, 600, 500); } - void addTreeMenuItem(final TreePanel treePanel, String title) + public void addTreeMenuItem(final TreePanel treePanel, String title) { final MenuItem item = new MenuItem(title); 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)); @@ -1139,12 +1562,12 @@ public class AlignFrame }); } - protected void documentation_actionPerformed(ActionEvent e) + protected void documentation_actionPerformed() { - jalview.bin.JalviewLite.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 @@ -1208,4 +1631,520 @@ public class AlignFrame jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200); } + + public void showURL(String url, String target) + { + if (applet == null) + { + System.out.println("Not running as applet - no browser available."); + } + else + { + try + { + applet.getAppletContext().showDocument(new java.net.URL(url), + target); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + + ////////////////////////////////////////////////////////////////////////////////// + //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 MenuItem remove2LeftMenuItem = new MenuItem(); + protected MenuItem remove2RightMenuItem = new MenuItem(); + protected MenuItem removeGappedColumnMenuItem = new MenuItem(); + protected MenuItem removeAllGapsMenuItem = new MenuItem(); + protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem(); + protected MenuItem sortPairwiseMenuItem = new MenuItem(); + protected MenuItem sortIDMenuItem = new MenuItem(); + protected MenuItem sortGroupMenuItem = new MenuItem(); + protected MenuItem removeRedundancyMenuItem = new MenuItem(); + protected MenuItem pairwiseAlignmentMenuItem = new MenuItem(); + protected MenuItem PCAMenuItem = new MenuItem(); + protected MenuItem averageDistanceTreeMenuItem = new MenuItem(); + protected MenuItem neighbourTreeMenuItem = new MenuItem(); + BorderLayout borderLayout1 = new BorderLayout(); + public Label statusBar = new Label(); + protected Menu outputTextboxMenu = new Menu(); + protected MenuItem clustalColour = new MenuItem(); + protected MenuItem zappoColour = new MenuItem(); + protected MenuItem taylorColour = new MenuItem(); + protected MenuItem hydrophobicityColour = new MenuItem(); + protected MenuItem helixColour = new MenuItem(); + protected MenuItem strandColour = new MenuItem(); + protected MenuItem turnColour = new MenuItem(); + protected MenuItem buriedColour = new MenuItem(); + protected MenuItem userDefinedColour = new MenuItem(); + protected MenuItem PIDColour = new MenuItem(); + protected MenuItem BLOSUM62Colour = new MenuItem(); + MenuItem njTreeBlosumMenuItem = new MenuItem(); + MenuItem avDistanceTreeBlosumMenuItem = new MenuItem(); + protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem(); + MenuItem overviewMenuItem = new MenuItem(); + protected MenuItem undoMenuItem = new MenuItem(); + protected MenuItem redoMenuItem = new MenuItem(); + protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem(); + MenuItem noColourmenuItem = new MenuItem(); + protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem(); + protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem(); + MenuItem findMenuItem = new MenuItem(); + Menu searchMenu = new Menu(); + protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem(); + protected MenuItem nucleotideColour = new MenuItem(); + MenuItem deleteGroups = new MenuItem(); + MenuItem delete = new MenuItem(); + MenuItem copy = new MenuItem(); + MenuItem cut = new MenuItem(); + Menu pasteMenu = new Menu(); + MenuItem pasteNew = new MenuItem(); + MenuItem pasteThis = new MenuItem(); + protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem(); + protected MenuItem font = new MenuItem(); + protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem(); + protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); + MenuItem modifyPID = new MenuItem(); + MenuItem modifyConservation = new MenuItem(); + protected Menu sortByTreeMenu = new Menu(); + Menu sort = new Menu(); + Menu calculate = new Menu(); + MenuItem inputText = new MenuItem(); + Menu helpMenu = new Menu(); + MenuItem documentation = new MenuItem(); + MenuItem about = new MenuItem(); + protected CheckboxMenuItem seqLimits = new CheckboxMenuItem(); + Panel embeddedMenu; + Label embeddedEdit; + Label 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++) + { + + item = new MenuItem( (String) jalview.io.AppletFormatAdapter.formats. + elementAt( + i)); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outputText_actionPerformed(e); + } + }); + + 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"); + selectAllSequenceMenuItem.addActionListener(this); + deselectAllSequenceMenuItem.setLabel("Deselect All"); + deselectAllSequenceMenuItem.addActionListener(this); + invertSequenceMenuItem.setLabel("Invert Selection"); + invertSequenceMenuItem.addActionListener(this); + remove2LeftMenuItem.setLabel("Remove Left"); + remove2LeftMenuItem.addActionListener(this); + remove2RightMenuItem.setLabel("Remove Right"); + remove2RightMenuItem.addActionListener(this); + removeGappedColumnMenuItem.setLabel("Remove Empty Columns"); + removeGappedColumnMenuItem.addActionListener(this); + removeAllGapsMenuItem.setLabel("Remove All Gaps"); + removeAllGapsMenuItem.addActionListener(this); + viewBoxesMenuItem.setLabel("Boxes"); + viewBoxesMenuItem.setState(true); + viewBoxesMenuItem.addItemListener(this); + viewTextMenuItem.setLabel("Text"); + viewTextMenuItem.setState(true); + viewTextMenuItem.addItemListener(this); + sortPairwiseMenuItem.setLabel("by Pairwise Identity"); + sortPairwiseMenuItem.addActionListener(this); + sortIDMenuItem.setLabel("by ID"); + sortIDMenuItem.addActionListener(this); + sortGroupMenuItem.setLabel("by Group"); + sortGroupMenuItem.addActionListener(this); + removeRedundancyMenuItem.setLabel("Remove Redundancy..."); + removeRedundancyMenuItem.addActionListener(this); + pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments..."); + pairwiseAlignmentMenuItem.addActionListener(this); + PCAMenuItem.setLabel("Principal Component Analysis"); + PCAMenuItem.addActionListener(this); + averageDistanceTreeMenuItem.setLabel( + "Average Distance Using % Identity"); + averageDistanceTreeMenuItem.addActionListener(this); + neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity"); + neighbourTreeMenuItem.addActionListener(this); + alignFrameMenuBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setBackground(Color.white); + statusBar.setFont(new java.awt.Font("Verdana", 0, 11)); + statusBar.setText("Status bar"); + outputTextboxMenu.setLabel("Output to Textbox"); + clustalColour.setLabel("Clustalx"); + + clustalColour.addActionListener(this); + zappoColour.setLabel("Zappo"); + zappoColour.addActionListener(this); + taylorColour.setLabel("Taylor"); + taylorColour.addActionListener(this); + hydrophobicityColour.setLabel("Hydrophobicity"); + hydrophobicityColour.addActionListener(this); + helixColour.setLabel("Helix Propensity"); + helixColour.addActionListener(this); + strandColour.setLabel("Strand Propensity"); + strandColour.addActionListener(this); + turnColour.setLabel("Turn Propensity"); + turnColour.addActionListener(this); + buriedColour.setLabel("Buried Index"); + buriedColour.addActionListener(this); + userDefinedColour.setLabel("User Defined..."); + userDefinedColour.addActionListener(this); + PIDColour.setLabel("Percentage Identity"); + PIDColour.addActionListener(this); + BLOSUM62Colour.setLabel("BLOSUM62 Score"); + BLOSUM62Colour.addActionListener(this); + avDistanceTreeBlosumMenuItem.setLabel( + "Average Distance Using BLOSUM62"); + avDistanceTreeBlosumMenuItem.addActionListener(this); + njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62"); + njTreeBlosumMenuItem.addActionListener(this); + annotationPanelMenuItem.setLabel("Show Annotations"); + annotationPanelMenuItem.addItemListener(this); + colourTextMenuItem.setLabel("Colour Text"); + colourTextMenuItem.addItemListener(this); + overviewMenuItem.setLabel("Overview Window"); + overviewMenuItem.addActionListener(this); + undoMenuItem.setEnabled(false); + undoMenuItem.setLabel("Undo"); + undoMenuItem.addActionListener(this); + redoMenuItem.setEnabled(false); + redoMenuItem.setLabel("Redo"); + redoMenuItem.addActionListener(this); + conservationMenuItem.setLabel("by Conservation"); + conservationMenuItem.addItemListener(this); + noColourmenuItem.setLabel("None"); + noColourmenuItem.addActionListener(this); + wrapMenuItem.setLabel("Wrap"); + wrapMenuItem.addItemListener(this); + renderGapsMenuItem.setLabel("Show Gaps"); + renderGapsMenuItem.setState(true); + renderGapsMenuItem.addItemListener(this); + findMenuItem.setLabel("Find..."); + findMenuItem.addActionListener(this); + searchMenu.setLabel("Search"); + + abovePIDThreshold.setLabel("Above Identity Threshold"); + abovePIDThreshold.addItemListener(this); + nucleotideColour.setLabel("Nucleotide"); + nucleotideColour.addActionListener(this); + deleteGroups.setLabel("Undefine Groups"); + deleteGroups.addActionListener(this); + copy.setLabel("Copy"); + copy.addActionListener(this); + cut.setLabel("Cut"); + cut.addActionListener(this); + delete.setLabel("Delete"); + delete.addActionListener(this); + pasteMenu.setLabel("Paste"); + pasteNew.setLabel("To New Alignment"); + pasteNew.addActionListener(this); + pasteThis.setLabel("Add To This Alignment"); + pasteThis.addActionListener(this); + applyToAllGroups.setLabel("Apply Colour To All Groups"); + applyToAllGroups.setState(true); + applyToAllGroups.addItemListener(this); + font.setLabel("Font..."); + font.addActionListener(this); + scaleAbove.setLabel("Scale Above"); + scaleAbove.setState(true); + scaleAbove.setEnabled(false); + scaleAbove.addItemListener(this); + scaleLeft.setEnabled(false); + scaleLeft.setState(true); + scaleLeft.setLabel("Scale Left"); + scaleLeft.addItemListener(this); + scaleRight.setEnabled(false); + scaleRight.setState(true); + scaleRight.setLabel("Scale Right"); + scaleRight.addItemListener(this); + modifyPID.setLabel("Modify Identity Threshold..."); + modifyPID.addActionListener(this); + modifyConservation.setLabel("Modify Conservation Threshold..."); + modifyConservation.addActionListener(this); + sortByTreeMenu.setLabel("By Tree Order"); + sort.setLabel("Sort"); + calculate.setLabel("Calculate Tree"); + inputText.setLabel("Input from textbox"); + inputText.addActionListener(this); + + helpMenu.setLabel("Help"); + documentation.setLabel("Documentation"); + documentation.addActionListener(this); + + about.setLabel("About..."); + about.addActionListener(this); + seqLimits.setState(true); + seqLimits.setLabel("Show Sequence Limits"); + seqLimits.addItemListener(this); + featureSettings.setLabel("Feature Settings..."); + featureSettings.addActionListener(this); + sequenceFeatures.setLabel("Sequence Features"); + sequenceFeatures.addItemListener(this); + sequenceFeatures.setState(true); + + alignFrameMenuBar.add(fileMenu); + alignFrameMenuBar.add(editMenu); + alignFrameMenuBar.add(searchMenu); + alignFrameMenuBar.add(viewMenu); + alignFrameMenuBar.add(colourMenu); + alignFrameMenuBar.add(calculateMenu); + alignFrameMenuBar.add(helpMenu); + fileMenu.add(inputText); + fileMenu.add(outputTextboxMenu); + fileMenu.addSeparator(); + fileMenu.add(closeMenuItem); + editMenu.add(undoMenuItem); + editMenu.add(redoMenuItem); + editMenu.add(cut); + editMenu.add(copy); + editMenu.add(pasteMenu); + editMenu.add(delete); + editMenu.addSeparator(); + editMenu.add(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.addSeparator(); + viewMenu.add(overviewMenuItem); + colourMenu.add(applyToAllGroups); + colourMenu.addSeparator(); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideColour); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(conservationMenuItem); + colourMenu.add(modifyConservation); + colourMenu.add(abovePIDThreshold); + colourMenu.add(modifyPID); + calculateMenu.add(sort); + calculateMenu.add(calculate); + calculateMenu.addSeparator(); + calculateMenu.add(pairwiseAlignmentMenuItem); + calculateMenu.add(PCAMenuItem); + this.add(statusBar, BorderLayout.SOUTH); + pasteMenu.add(pasteNew); + pasteMenu.add(pasteThis); + sort.add(sortIDMenuItem); + sort.add(sortByTreeMenu); + sort.add(sortGroupMenuItem); + sort.add(sortPairwiseMenuItem); + calculate.add(averageDistanceTreeMenuItem); + calculate.add(neighbourTreeMenuItem); + calculate.add(avDistanceTreeBlosumMenuItem); + calculate.add(njTreeBlosumMenuItem); + helpMenu.add(documentation); + helpMenu.add(about); + } + + 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(2); // Seperator + + applet.setLayout(new BorderLayout()); + applet.add(embeddedMenu, BorderLayout.NORTH); + applet.add(statusBar, BorderLayout.SOUTH); + applet.validate(); + + + alignPanel.setSize(applet.size().width, applet.size().height + - embeddedMenu.HEIGHT - statusBar.HEIGHT); + + applet.add(alignPanel, BorderLayout.CENTER); + applet.validate(); + } + + + + PopupMenu filePopup, editPopup, searchPopup, + viewPopup, colourPopup, calculatePopup, helpPopup; + MenuItem featureSettings = new MenuItem(); + CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem(); + + 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