import java.util.*;\r
import java.io.InputStreamReader;\r
import java.io.BufferedReader;\r
+import java.net.URL;\r
\r
public class AlignFrame\r
extends GAlignFrame\r
{\r
final AlignmentPanel alignPanel;\r
final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
+ int NEW_WINDOW_WIDTH = 700;\r
+ int NEW_WINDOW_HEIGHT = 500;\r
jalview.bin.JalviewLite applet;\r
\r
- public AlignFrame(AlignmentI al)\r
+\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title)\r
{\r
- this.applet = null;\r
- viewport = new AlignViewport(al, null);\r
+ this.applet = applet;\r
+ viewport = new AlignViewport(al, applet);\r
alignPanel = new AlignmentPanel(this, viewport);\r
add(alignPanel);\r
alignPanel.validate();\r
\r
- this.addWindowListener(new WindowAdapter()\r
+ if(applet!=null)\r
{\r
- public void windowClosing(WindowEvent e)\r
+ String treeFile = applet.getParameter("treeFile");\r
+ if (treeFile != null)\r
{\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ try\r
+ {\r
+ jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
+ getCodeBase() + treeFile, "URL");\r
+ fin.parse();\r
\r
- }\r
+ if (fin.getTree() != null)\r
+ {\r
+ TreePanel tp = null;\r
+ tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
+ fin, "FromFile", applet.getCodeBase() + treeFile);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ sortIDMenuItem_actionPerformed(null);\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ sortPairwiseMenuItem_actionPerformed(null);\r
+ }\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
- {\r
- this.applet = applet;\r
- viewport = new AlignViewport(al, applet);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed(null);\r
+ }\r
+ }\r
\r
- String treeFile = applet.getParameter("treeFile");\r
- if (treeFile != null)\r
- {\r
try\r
{\r
- treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
- fin.parse();\r
-\r
- if (fin.getTree() != null)\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ NEW_WINDOW_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
{\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
+ int height = Integer.parseInt(param);\r
+ NEW_WINDOW_HEIGHT = height;\r
}\r
}\r
catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ {}\r
+\r
}\r
\r
this.addWindowListener(new WindowAdapter()\r
}\r
});\r
\r
+ viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(java.beans.PropertyChangeEvent evt)\r
+ {\r
+ if (evt.getPropertyName().equals("alignment"))\r
+ {\r
+ alignmentChanged();\r
+ }\r
+ }\r
+ });\r
+\r
+ jalview.bin.JalviewLite.addFrame(this, title,\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
\r
\r
}\r
\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file)\r
+ {\r
+ try\r
+ {\r
+ URL url = new URL(file);\r
+\r
+ BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()));\r
+ SequenceI seq = null;\r
+ String line, type, desc, token;\r
+\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceFeature sf;\r
+ FeatureRenderer fr = alignPanel.seqPanel.seqCanvas.getFeatureRenderer();\r
+ int lineNo = 0;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ lineNo++;\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() == 2)\r
+ {\r
+ type = st.nextToken();\r
+ UserColourScheme ucs = new UserColourScheme(st.nextToken());\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ continue;\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ desc = st.nextToken();\r
+ token = st.nextToken();\r
+ if (!token.equals("ID_NOT_SPECIFIED"))\r
+ {\r
+ index = viewport.alignment.findIndex(viewport.alignment.findName(\r
+ token));\r
+ st.nextToken();\r
+ }\r
+ else\r
+ {\r
+ index = Integer.parseInt(st.nextToken());\r
+ }\r
+\r
+ start = Integer.parseInt(st.nextToken());\r
+ end = Integer.parseInt(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ type = st.nextToken();\r
+\r
+ if(fr.getColour(type)==null)\r
+ {\r
+ // Probably the old style groups file\r
+ UserColourScheme ucs = new UserColourScheme(type);\r
+ fr.setColour(type, ucs.findColour("A"));\r
+ }\r
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+ }\r
+ }\r
+\r
+ viewport.showSequenceFeatures = true;\r
+ ((Alignment)viewport.alignment).featuresAdded = true;\r
+\r
+ alignPanel.repaint();\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+\r
public void inputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame,\r
"Alignment output - " + e.getActionCommand(),\r
600, 500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().\r
- getSequences()));\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment().getSequences(),\r
+ viewport.showDBPrefix,\r
+ viewport.showJVSuffix));\r
}\r
\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
PaintRefresher.components.remove(viewport.alignment);\r
dispose();\r
+ if(PaintRefresher.components.size()==0 && applet==null)\r
+ System.exit(0);\r
}\r
\r
Stack historyList = new Stack();\r
redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
HistoryItem.HIDE));\r
restoreHistoryItem(hi);\r
- resetAllColourSchemes();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
restoreHistoryItem(hi);\r
updateEditMenuBar();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
// used by undo and redo\r
\r
updateEditMenuBar();\r
\r
- viewport.updateConsensus();\r
- viewport.updateConservation();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
String newtitle = new String("Copied sequences");\r
if (getTitle().startsWith("Copied sequences"))\r
{\r
{\r
newtitle = newtitle.concat("- from " + getTitle());\r
}\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet, newtitle);\r
+\r
jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
NEW_WINDOW_HEIGHT);\r
}\r
{\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
catch (Exception ex)\r
{}\r
}\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
\r
}\r
\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.repaint();\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
}\r
\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
-\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
}\r
\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
\r
- viewport.updateConservation();\r
- viewport.updateConsensus();\r
- resetAllColourSchemes();\r
- alignPanel.repaint();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes();\r
+ end = viewport.getSelectionGroup().getEndRes()+1;\r
}\r
else\r
seqs = viewport.alignment.getSequences();\r
\r
- for (int i = 0; i <seqs.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- current = (SequenceI)seqs.elementAt(i);\r
+ current = (SequenceI) seqs.elementAt(i);\r
jSize = current.getLength();\r
\r
+ // Removing a range is much quicker than removing gaps\r
+ // one by one for long sequences\r
int j = start;\r
+ int rangeStart=-1, rangeEnd=-1;\r
+\r
do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
{\r
- current.deleteCharAt(j);\r
- j--;\r
- jSize--;\r
+ if(rangeStart==-1)\r
+ {\r
+ rangeStart = j;\r
+ rangeEnd = j+1;\r
+ }\r
+ else\r
+ {\r
+ rangeEnd++;\r
+ }\r
+ j++;\r
+ }\r
+ else\r
+ {\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ j-=rangeEnd-rangeStart;\r
+ jSize-=rangeEnd-rangeStart;\r
+ rangeStart = -1;\r
+ rangeEnd = -1;\r
+ }\r
+ else\r
+ j++;\r
}\r
- j++;\r
}\r
- while(j < end && j < jSize) ;\r
+ while (j < end && j < jSize);\r
+ if(rangeStart>-1)\r
+ {\r
+ current.deleteChars(rangeStart, rangeEnd);\r
+ }\r
}\r
-\r
viewport.setStartRes(seq.findIndex(startRes)-1);\r
- viewport.updateConservation();\r
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ }\r
+\r
+ public void alignmentChanged()\r
+ {\r
viewport.updateConsensus();\r
+ viewport.updateConservation ();\r
resetAllColourSchemes();\r
+ if(alignPanel.overviewPanel!=null)\r
+ alignPanel.overviewPanel.updateOverviewImage();\r
alignPanel.repaint();\r
}\r
\r
ColourSchemeI cs = viewport.globalColourScheme;\r
if(cs!=null)\r
{\r
- cs.setConsensus(viewport.vconsensus);\r
- if(cs.conservationApplied())\r
- {\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
+ if (cs instanceof ClustalxColourScheme)\r
+ {\r
+ ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
+ resetClustalX(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth());\r
+ }\r
\r
- cs.setConservation(c);\r
- }\r
- }\r
+ cs.setConsensus(viewport.vconsensus);\r
+ if (cs.conservationApplied())\r
+ {\r
+ Alignment al = (Alignment) viewport.alignment;\r
+ Conservation c = new Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ al.getSequences(), 0,\r
+ al.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, viewport.ConsPercGaps);\r
\r
- if(viewport.getGlobalColourScheme()!=null\r
- && viewport.getGlobalColourScheme() instanceof ClustalxColourScheme)\r
- {\r
- ((ClustalxColourScheme)viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
+ cs.setConservation(c);\r
+ }\r
}\r
\r
int s, sSize = viewport.alignment.getGroups().size();\r
{\r
((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
}\r
-\r
sg.recalcConservation();\r
-\r
}\r
}\r
\r
\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
- Finder finder = new Finder(alignPanel);\r
+ new Finder(alignPanel);\r
}\r
\r
public void font_actionPerformed(ActionEvent e)\r
{\r
- Frame frame = new Frame();\r
- FontChooser fc = new FontChooser(alignPanel, frame);\r
- frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
+ new FontChooser(alignPanel);\r
+ }\r
\r
+ public void dbref_actionPerformed(ItemEvent e)\r
+ {\r
+ viewport.showDBPrefix = dbref.getState();\r
+ alignPanel.fontChanged();\r
+ alignPanel.repaint();\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ public void seqLimits_itemStateChanged(ItemEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.getState());\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
alignPanel.repaint();\r
}\r
\r
+\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
- if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setState(false);\r
- return;\r
- }\r
viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
}\r
\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
+ new UserDefinedColours(alignPanel, null);\r
}\r
\r
public void PIDColour_actionPerformed(ActionEvent e)\r
if (viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
- frame.add(new PairwiseAlignPanel(viewport));\r
+ frame.add(new PairwiseAlignPanel(alignPanel));\r
jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600, 500);\r
}\r
}\r
\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.repaint();\r
+ }\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
viewport.getSelectionGroup().getSize() < 4 &&\r
\r
try\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport, null);\r
- Frame frame = new Frame();\r
- frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
- 400, 400);\r
+ new PCAPanel(viewport);\r
}\r
catch (java.lang.OutOfMemoryError ex)\r
{\r
\r
protected void documentation_actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html");\r
}\r
\r
protected void about_actionPerformed(ActionEvent e)\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
+\r
+ /**\r
+ * Displays the given URL in a new browser window\r
+ *\r
+ * @param url URL to display in browser window.\r
+ * <br>New window will be named "HELP_WINDOW"\r
+ */\r
+ public void showURL(String url)\r
+ {\r
+ showURL(url, "HELP");\r
+ }\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff