X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=2b53d7672379948c423b3f0ca158c2fe8e183c4a;hb=7bc213bae5828287329a3490faba291706599b03;hp=189a36dbea09b04eb54cd4bf64d06233e308cf34;hpb=1db1f53588cf74844c414838eda44015a5bfdf70;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 189a36d..2b53d76 100755 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -40,12 +40,17 @@ public class AlignFrame extends Frame implements ActionListener, int NEW_WINDOW_HEIGHT = 500; jalview.bin.JalviewLite applet; + String jalviewServletURL; + public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded) { + + jalviewServletURL = applet.getParameter("APPLICATION_URL"); + try{ jbInit(); }catch(Exception ex) @@ -59,6 +64,8 @@ public class AlignFrame extends Frame implements ActionListener, annotationPanelMenuItem.setState(viewport.showAnnotation); + seqLimits.setState(viewport.showJVSuffix); + if(applet!=null) { String param = applet.getParameter("sortBy"); @@ -148,108 +155,44 @@ public class AlignFrame extends Frame implements ActionListener, * @param String DOCUMENT ME! */ - public void parseFeaturesFile(String file) + public void parseFeaturesFile(String file, String type) { - String line = null; - 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) { - BufferedReader in = null; - java.io.InputStream is = getClass().getResourceAsStream("/" + file); - if (is != null) - { - in = new BufferedReader(new java.io.InputStreamReader(is)); - } - else - { - URL url = new URL(file); - in = new BufferedReader(new InputStreamReader(url.openStream())); - } - - SequenceI seq = null; - String type, desc, token; - - int index, start, end; - StringTokenizer st; - SequenceFeature sf; - FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer(); - int lineNo = 0; - String featureGroup = null; - while ( (line = in.readLine()) != null) - { - lineNo++; - st = new StringTokenizer(line, "\t"); - if (st.countTokens() == 2) - { - type = st.nextToken(); - if(type.equalsIgnoreCase("startgroup")) - { - featureGroup = st.nextToken(); - } - else if(type.equalsIgnoreCase("endgroup")) - { - //We should check whether this is the current group, - //but at present theres no way of showing more than 1 group - st.nextToken(); - featureGroup = null; - } - else - { - 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); - - 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, featureGroup); - - seq.addSequenceFeature(sf); - } - } + ex.printStackTrace(); + } + if(featuresFile) + { + if(featureLinks.size()>0) + alignPanel.seqPanel.seqCanvas + .getFeatureRenderer().featureLinks = featureLinks; viewport.showSequenceFeatures = true; sequenceFeatures.setState(true); - alignPanel.repaint(); - - } - catch (Exception ex) - { - ex.printStackTrace(); - System.out.println("Error parsing groups file: " + ex +"\n"+line); } + } + 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 @@ -262,6 +205,10 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: + if (viewport.cursorMode && !evt.isControlDown()) + { + alignPanel.seqPanel.setCursorColumn(); + } if (evt.isControlDown() || evt.isMetaDown()) { copy_actionPerformed(); @@ -280,21 +227,108 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_DOWN: - moveSelectedSequences(false); + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,1); + } + else + moveSelectedSequences(false); break; + case KeyEvent.VK_UP: - moveSelectedSequences(true); + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(0,-1); + } + else + moveSelectedSequences(true); + break; + + case KeyEvent.VK_LEFT: + if(viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(-1,0); + } + break; + + case KeyEvent.VK_RIGHT: + if (viewport.cursorMode) + { + alignPanel.seqPanel.moveCursor(1,0); + } + break; + case KeyEvent.VK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()); + } break; + + case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: + if(viewport.cursorMode) + { + alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); + } + else + { + cut_actionPerformed(); + alignPanel.seqPanel.seqCanvas.repaint(); + } + break; + + case KeyEvent.VK_S: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRow(); + } + break; + case KeyEvent.VK_P: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorPosition(); + } + break; + + case KeyEvent.VK_ENTER: + case KeyEvent.VK_COMMA: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setCursorRowAndColumn(); + } + break; + + case KeyEvent.VK_Q: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(true); + } + break; + case KeyEvent.VK_M: + if(viewport.cursorMode) + { + alignPanel.seqPanel.setSelectionAreaAtCursor(false); + } + break; + + case KeyEvent.VK_F2: + viewport.cursorMode = ! viewport.cursorMode; + statusBar.setText("Keyboard editing mode is "+ + (viewport.cursorMode ? "on" : "off")); + if(viewport.cursorMode) + { + alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes; + alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq; + } + alignPanel.seqPanel.seqCanvas.repaint(); + 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) @@ -335,6 +369,8 @@ public void itemStateChanged(ItemEvent evt) abovePIDThreshold_actionPerformed(); else if(evt.getSource()==applyToAllGroups) applyToAllGroups_actionPerformed(); + else if(evt.getSource()==autoCalculate) + viewport.autocalculateConsensus = autoCalculate.getState(); } public void actionPerformed(ActionEvent evt) { @@ -342,6 +378,8 @@ public void itemStateChanged(ItemEvent evt) inputText_actionPerformed(); else if(evt.getSource()==loadTree) loadTree_actionPerformed(); + else if(evt.getSource()==loadApplication) + launchFullApplication(); else if(evt.getSource()==closeMenuItem) closeMenuItem_actionPerformed(); else if(evt.getSource()==copy) @@ -472,6 +510,63 @@ public void itemStateChanged(ItemEvent evt) viewport.showJVSuffix)); } + void launchFullApplication() + { + StringBuffer url = new StringBuffer(jalviewServletURL); + + url.append("?open="+ + appendProtocol( applet.getParameter("file") ) ); + + if(applet.getParameter("features")!=null) + { + url.append( "&features=" ); + url.append( appendProtocol( applet.getParameter("features") ) ); + } + + if(applet.getParameter("defaultColour")!=null) + { + url.append("&colour=" + + removeWhiteSpace(applet.getParameter("defaultColour")) + ); + } + + if(applet.getParameter("userDefinedColour")!=null) + { + url.append( "&colour=" + + removeWhiteSpace( 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 = applet.getCodeBase()+url; + } + return url; + } + public void closeMenuItem_actionPerformed() { PaintRefresher.components.remove(viewport.alignment); @@ -557,13 +652,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = 1; i < viewport.alignment.getHeight(); i++) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(false).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i - 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(false).contains(temp)) { continue; } @@ -577,13 +672,13 @@ public void itemStateChanged(ItemEvent evt) for (int i = viewport.alignment.getHeight() - 2; i > -1; i--) { SequenceI seq = viewport.alignment.getSequenceAt(i); - if (!sg.sequences.contains(seq)) + if (!sg.getSequences(true).contains(seq)) { continue; } SequenceI temp = viewport.alignment.getSequenceAt(i + 1); - if (sg.sequences.contains(temp)) + if (sg.getSequences(true).contains(temp)) { continue; } @@ -607,7 +702,7 @@ public void itemStateChanged(ItemEvent evt) 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); @@ -617,7 +712,7 @@ public void itemStateChanged(ItemEvent evt) int index = 0, startRes, endRes; char ch; - for (int i = 0; i < sg.getSize(); i++) + for (int i = 0; i < sg.getSize(false); i++) { SequenceI seq = null; @@ -763,10 +858,10 @@ public void itemStateChanged(ItemEvent evt) 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); @@ -829,6 +924,11 @@ public void itemStateChanged(ItemEvent evt) public void deselectAllSequenceMenuItem_actionPerformed() { + if(viewport.cursorMode) + { + alignPanel.seqPanel.keyboardNo1=null; + alignPanel.seqPanel.keyboardNo2=null; + } viewport.setSelectionGroup(null); viewport.getColumnSelection().clear(); viewport.setSelectionGroup(null); @@ -942,10 +1042,10 @@ public void itemStateChanged(ItemEvent evt) 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; } @@ -1003,8 +1103,13 @@ public void itemStateChanged(ItemEvent evt) 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(); @@ -1046,7 +1151,8 @@ public void itemStateChanged(ItemEvent evt) 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(); } @@ -1282,7 +1388,7 @@ public void itemStateChanged(ItemEvent evt) } if (cs instanceof ClustalxColourScheme) { - sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth()); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), sg.getWidth()); } else { @@ -1302,7 +1408,7 @@ public void itemStateChanged(ItemEvent evt) || cs instanceof Blosum62ColourScheme) { sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus()); - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth())); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, sg.getWidth())); } else sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus()); @@ -1311,7 +1417,7 @@ public void itemStateChanged(ItemEvent evt) { 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); @@ -1424,17 +1530,12 @@ public void itemStateChanged(ItemEvent evt) public void removeRedundancyMenuItem_actionPerformed() { - RedundancyPanel sp = new RedundancyPanel(alignPanel); - Frame frame = new Frame(); - frame.add(sp); - jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection", - 400, 120); - + new RedundancyPanel(alignPanel); } public void pairwiseAlignmentMenuItem_actionPerformed() { - if (viewport.getSelectionGroup().getSize() > 1) + if (viewport.getSelectionGroup().getSize(false) > 1) { Frame frame = new Frame(); frame.add(new PairwiseAlignPanel(alignPanel)); @@ -1464,8 +1565,8 @@ public void itemStateChanged(ItemEvent evt) } 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; @@ -1523,19 +1624,9 @@ public void itemStateChanged(ItemEvent evt) } - final TreePanel tp; - if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) - { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, - pwType, - 0, viewport.alignment.getWidth()); - } - else - { - tp = new TreePanel(viewport, viewport.getAlignment().getSequences(), - type, pwType, 0, viewport.alignment.getWidth()); - } + final TreePanel tp = new TreePanel(viewport, + type, + pwType); addTreeMenuItem(tp, title); @@ -1544,8 +1635,6 @@ public void itemStateChanged(ItemEvent evt) void loadTree_actionPerformed() { - TreePanel tp = null; - CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this); cap.setText("Paste your Newick tree file here."); cap.treeImport = true; @@ -1557,8 +1646,9 @@ public void itemStateChanged(ItemEvent evt) public void loadTree(jalview.io.NewickFile tree, String treeFile) { TreePanel tp = new TreePanel(viewport, - viewport.getAlignment().getSequences(), - tree, "From File - ", treeFile); + treeFile, + "From File - ", + tree); jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500); addTreeMenuItem(tp, treeFile); } @@ -1623,7 +1713,7 @@ public void itemStateChanged(ItemEvent evt) g.drawString("If you use JalView, please cite:", x, y += fh + 8); g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"", x, y += fh); - g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh); + g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh); } } @@ -1667,6 +1757,7 @@ public void itemStateChanged(ItemEvent evt) { try { + System.out.println("Show url: "+url); applet.getAppletContext().showDocument(new java.net.URL(url), target); } @@ -1683,6 +1774,7 @@ public void itemStateChanged(ItemEvent evt) protected MenuBar alignFrameMenuBar = new MenuBar(); protected Menu fileMenu = new Menu("File"); + protected MenuItem loadApplication = new MenuItem("View in Full Application"); protected MenuItem loadTree = new MenuItem("Load Associated Tree"); protected MenuItem closeMenuItem = new MenuItem("Close"); protected Menu editMenu = new Menu("Edit"); @@ -1749,6 +1841,8 @@ public void itemStateChanged(ItemEvent evt) protected CheckboxMenuItem scaleRight = new CheckboxMenuItem(); MenuItem modifyPID = new MenuItem(); MenuItem modifyConservation = new MenuItem(); + protected CheckboxMenuItem autoCalculate + = new CheckboxMenuItem("Autocalculate Consensus", true); protected Menu sortByTreeMenu = new Menu(); Menu sort = new Menu(); Menu calculate = new Menu(); @@ -1791,6 +1885,7 @@ public void itemStateChanged(ItemEvent evt) outputTextboxMenu.add(item); } closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); @@ -1926,6 +2021,7 @@ public void itemStateChanged(ItemEvent evt) sortByTreeMenu.setLabel("By Tree Order"); sort.setLabel("Sort"); calculate.setLabel("Calculate Tree"); + autoCalculate.addItemListener(this); inputText.setLabel("Input from textbox"); inputText.addActionListener(this); @@ -1955,6 +2051,8 @@ public void itemStateChanged(ItemEvent evt) alignFrameMenuBar.add(helpMenu); fileMenu.add(inputText); fileMenu.add(outputTextboxMenu); + if(jalviewServletURL!=null) + fileMenu.add(loadApplication); fileMenu.addSeparator(); fileMenu.add(loadTree); fileMenu.add(closeMenuItem); @@ -2021,6 +2119,7 @@ public void itemStateChanged(ItemEvent evt) calculateMenu.addSeparator(); calculateMenu.add(pairwiseAlignmentMenuItem); calculateMenu.add(PCAMenuItem); + calculateMenu.add(autoCalculate); this.add(statusBar, BorderLayout.SOUTH); pasteMenu.add(pasteNew); pasteMenu.add(pasteThis); @@ -2084,7 +2183,7 @@ public void itemStateChanged(ItemEvent evt) // setVisible(false); fileMenu.remove(closeMenuItem); - fileMenu.remove(2); // Seperator + fileMenu.remove(3); // Seperator applet.setLayout(new BorderLayout()); applet.add(embeddedMenu, BorderLayout.NORTH);