X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=d1b2da99185f0add4f6f9999011ebd774f18a772;hb=8f599b2d8da5ad8ccfcd42139e1b6f170bc3ad0f;hp=6b7901852b17d2cafe75c1ca0b9404d4942e2768;hpb=49444a1e7e2cf192e386e28732175fd2cf59bbad;p=jalview.git diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 6b79018..d1b2da9 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"); @@ -148,106 +155,35 @@ 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 @@ -269,7 +205,7 @@ public class AlignFrame extends Frame implements ActionListener, } break; case KeyEvent.VK_C: - if (viewport.cursorMode) + if (viewport.cursorMode && !evt.isControlDown()) { alignPanel.seqPanel.setCursorColumn(); } @@ -329,14 +265,12 @@ public class AlignFrame extends Frame implements ActionListener, break; case KeyEvent.VK_DELETE: + case KeyEvent.VK_BACK_SPACE: if(viewport.cursorMode) { alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()); } - break; - - case KeyEvent.VK_BACK_SPACE: - if(!viewport.cursorMode) + else { cut_actionPerformed(); alignPanel.seqPanel.seqCanvas.repaint(); @@ -444,6 +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) @@ -574,6 +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); @@ -659,13 +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; } @@ -679,13 +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; } @@ -709,7 +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); @@ -719,7 +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; @@ -865,10 +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); @@ -1049,10 +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; } @@ -1158,7 +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(); } @@ -1394,7 +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 { @@ -1414,7 +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()); @@ -1423,7 +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); @@ -1536,17 +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)); @@ -1576,8 +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; @@ -1637,9 +1626,11 @@ public void itemStateChanged(ItemEvent evt) final TreePanel tp; if (viewport.getSelectionGroup() != null && - viewport.getSelectionGroup().getSize() > 3) + viewport.getSelectionGroup().getSize(false) > 3) { - tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type, + tp = new TreePanel(viewport, + viewport.getSelectionGroup().getSequences(false), + type, pwType, 0, viewport.alignment.getWidth()); } @@ -1656,8 +1647,6 @@ 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; @@ -1735,7 +1724,7 @@ 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); } } @@ -1779,6 +1768,7 @@ public void itemStateChanged(ItemEvent evt) { try { + System.out.println("Show url: "+url); applet.getAppletContext().showDocument(new java.net.URL(url), target); } @@ -1795,6 +1785,7 @@ 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"); @@ -1905,6 +1896,7 @@ public void itemStateChanged(ItemEvent evt) outputTextboxMenu.add(item); } closeMenuItem.addActionListener(this); + loadApplication.addActionListener(this); loadTree.addActionListener(this); selectAllSequenceMenuItem.addActionListener(this); @@ -2070,6 +2062,8 @@ 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); @@ -2200,7 +2194,7 @@ 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);