package jalview.gui;\r
\r
import java.beans.*;\r
+import java.io.*;\r
import java.util.*;\r
\r
import java.awt.*;\r
import jalview.schemes.*;\r
import jalview.ws.*;\r
\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class AlignFrame\r
extends GAlignFrame\r
{\r
+ /** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_WIDTH = 700;\r
+\r
+ /** DOCUMENT ME!! */\r
public static final int NEW_WINDOW_HEIGHT = 500;\r
final AlignmentPanel alignPanel;\r
final AlignViewport viewport;\r
- public String currentFileFormat = "Jalview";\r
+\r
+ /** DOCUMENT ME!! */\r
+ public String currentFileFormat = null;\r
Stack historyList = new Stack();\r
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
+ /**\r
+ * Creates a new AlignFrame object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
});\r
}\r
});\r
+ addServiceListeners();\r
}\r
\r
+ /* Set up intrinsic listeners for dynamically generated GUI bits. */\r
+ private void addServiceListeners()\r
+ {\r
+\r
+ final AlignFrame thisFrame = this;\r
+ final java.beans.PropertyChangeListener thisListener;\r
+ // Do this once to get current state\r
+ thisFrame.BuildWebServiceMenu();\r
+ Desktop.discoverer.addPropertyChangeListener(\r
+ thisListener = new java.beans.PropertyChangeListener()\r
+ {\r
+ public void propertyChange(PropertyChangeEvent evt)\r
+ {\r
+ // System.out.println("Discoverer property change.");\r
+ if (evt.getPropertyName().equals("services"))\r
+ {\r
+ // System.out.println("Rebuilding web service menu");\r
+ thisFrame.BuildWebServiceMenu();\r
+ }\r
+ }\r
+ });\r
+ addInternalFrameListener(new javax.swing.event.\r
+ InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ // System.out.println("deregistering discoverer listener");\r
+ Desktop.discoverer.removePropertyChangeListener(thisListener);\r
+ }\r
+ ;\r
+ });\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseGroupsFile(String file)\r
+ {\r
+ try\r
+ {\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ SequenceI seq = null;\r
+ String line, text, token;\r
+ UserColourScheme ucs;\r
+ int index, start, end;\r
+ StringTokenizer st;\r
+ SequenceGroup sg;\r
+ while ( (line = in.readLine()) != null)\r
+ {\r
+ st = new StringTokenizer(line, "\t");\r
+ if (st.countTokens() != 6)\r
+ {\r
+ System.out.println("Groups file " + file +\r
+ " is invalid. Read help file.");\r
+ System.exit(1);\r
+ }\r
+\r
+ while (st.hasMoreElements())\r
+ {\r
+ text = 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
+ ucs = new UserColourScheme(st.nextToken());\r
+\r
+ seq = viewport.alignment.getSequenceAt(index);\r
+ start = seq.findIndex(start) - 1;\r
+ end = seq.findIndex(end) - 1;\r
+\r
+ sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ sg.addSequence(seq, true);\r
+\r
+ viewport.alignment.addGroup(sg);\r
+ }\r
+ }\r
+\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error parsing groups file: " + ex);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void saveAlignmentMenu_actionPerformed(ActionEvent e)\r
{\r
JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT",\r
currentFileFormat);\r
\r
- if (currentFileFormat.equals("Jalview"))\r
- {\r
- String shortName = title;\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
\r
- if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
- {\r
- shortName = shortName.substring(shortName.lastIndexOf(\r
- java.io.File.separatorChar) + 1);\r
- }\r
+ saveAlignment(choice, currentFileFormat);\r
+ }\r
+ }\r
\r
- String choice = chooser.getSelectedFile().getPath();\r
- Jalview2XML.SaveAlignment(this, choice, shortName);\r
+ public boolean saveAlignment(String file, String format)\r
+ {\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ String shortName = title;\r
\r
- // USE Jalview2XML to save this file\r
- return;\r
+ if (shortName.indexOf(java.io.File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ java.io.File.separatorChar) + 1);\r
}\r
\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
+ Jalview2XML.SaveAlignment(this, file, shortName);\r
\r
- String output = FormatAdapter.formatSequences(currentFileFormat,\r
- viewport.getAlignment().getSequences());\r
+ // USE Jalview2XML to save this file\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ String output = FormatAdapter.formatSequences(format,\r
+ viewport.getAlignment().\r
+ getSequences());\r
+ if (output == null)\r
+ {\r
+ return false;\r
+ }\r
\r
try\r
{\r
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.\r
- FileWriter(\r
- choice));\r
+ java.io.PrintWriter out = new java.io.PrintWriter(\r
+ new java.io.FileWriter(file));\r
out.println(output);\r
out.close();\r
+ return true;\r
}\r
catch (Exception ex)\r
{\r
+ ex.printStackTrace();\r
}\r
}\r
+ return false;\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void outputText_actionPerformed(ActionEvent e)\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
getSequences()));\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
new HTMLOutput(viewport);\r
}\r
\r
- protected void createPNG_actionPerformed(ActionEvent e)\r
+ public void createImageMap(File file, String image)\r
+ {\r
+ alignPanel.makePNGImageMap(file, image);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createPNG(File f)\r
{\r
- alignPanel.makePNG();\r
+ alignPanel.makePNG(f);\r
}\r
\r
- protected void epsFile_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void createEPS(File f)\r
{\r
- alignPanel.makeEPS();\r
+ alignPanel.makeEPS(f);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void printMenuItem_actionPerformed(ActionEvent e)\r
{\r
//Putting in a thread avoids Swing painting problems\r
thread.start();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void closeMenuItem_actionPerformed(ActionEvent e)\r
{\r
try\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void updateEditMenuBar()\r
{\r
if (historyList.size() > 0)\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param hi DOCUMENT ME!\r
+ */\r
public void addHistoryItem(HistoryItem hi)\r
{\r
historyList.push(hi);\r
updateEditMenuBar();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void undoMenuItem_actionPerformed(ActionEvent e)\r
{\r
HistoryItem hi = (HistoryItem) historyList.pop();\r
restoreHistoryItem(hi);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void redoMenuItem_actionPerformed(ActionEvent e)\r
{\r
HistoryItem hi = (HistoryItem) redoList.pop();\r
viewport.getAlignment().getSequences());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param up DOCUMENT ME!\r
+ */\r
public void moveSelectedSequences(boolean up)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void copy_actionPerformed(ActionEvent e)\r
{\r
if (viewport.getSelectionGroup() == null)\r
orderedSeqs.put(index + "", seq);\r
}\r
\r
- int index = 0;\r
+ int index = 0, startRes, endRes;\r
+ char ch;\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
index++;\r
}\r
}\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
+\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
+\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
\r
buffer.append(seq.getName() + "\t" +\r
- seq.findPosition(sg.getStartRes()) + "\t" +\r
- seq.findPosition(sg.getEndRes()) + "\t" +\r
- sg.getSequenceAt(i).getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequence(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
c.setContents(new StringSelection(buffer.toString()), null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void pasteNew_actionPerformed(ActionEvent e)\r
{\r
paste(true);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void pasteThis_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
paste(false);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newAlignment DOCUMENT ME!\r
+ */\r
void paste(boolean newAlignment)\r
{\r
try\r
// could be anything being pasted in here\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void cut_actionPerformed(ActionEvent e)\r
{\r
copy_actionPerformed(null);\r
delete_actionPerformed(null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void delete_actionPerformed(ActionEvent e)\r
{\r
boolean seqsdeleted = false;\r
HistoryItem.HIDE));\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
+ boolean allSequences = false;\r
+ if (sg.sequences.size() == viewport.alignment.getHeight())\r
+ {\r
+ allSequences = true;\r
+ }\r
\r
for (int i = 0; i < sg.sequences.size(); i++)\r
{\r
int index = viewport.getAlignment().findIndex(seq);\r
seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (allSequences)\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
+\r
if (seq.getSequence().length() < 1)\r
{\r
seqsdeleted = true;\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void deleteGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.alignment.deleteAllGroups();\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = new SequenceGroup();\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
\r
- sg.setEndRes(viewport.alignment.getWidth());\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
viewport.setSelectionGroup(sg);\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
- alignPanel.annotationPanel.activeRes=null;\r
+ alignPanel.annotationPanel.activeRes = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- if(sg==null)\r
+\r
+ if (sg == null)\r
{\r
selectAllSequenceMenuItem_actionPerformed(null);\r
+\r
return;\r
}\r
\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
SequenceI current;\r
int jSize;\r
\r
- Vector seqs=null;\r
+ Vector seqs = null;\r
\r
- int start=0, end = viewport.alignment.getWidth();\r
+ int start = 0;\r
+ int end = viewport.alignment.getWidth();\r
\r
- if(viewport.getSelectionGroup()!=null)\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().sequences != null\r
+ && viewport.getSelectionGroup().sequences.size() > 0)\r
{\r
seqs = viewport.getSelectionGroup().sequences;\r
start = viewport.getSelectionGroup().getStartRes();\r
end = viewport.getSelectionGroup().getEndRes();\r
}\r
else\r
+ {\r
seqs = viewport.alignment.getSequences();\r
+ }\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
int j = start;\r
+\r
do\r
{\r
if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
}\r
j++;\r
}\r
- while(j < end);\r
+ while (j < end && j < jSize);\r
}\r
\r
viewport.updateConservation();\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void padGapsMenuitem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Pad Gaps", viewport.alignment,\r
\r
if (current.getLength() < Width)\r
{\r
- current.insertCharAt(Width-1, viewport.getGapCharacter());\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
}\r
}\r
\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void findMenuItem_actionPerformed(ActionEvent e)\r
{\r
JInternalFrame frame = new JInternalFrame();\r
frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void font_actionPerformed(ActionEvent e)\r
{\r
FontChooser fc = new FontChooser(alignPanel);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void fullSeqId_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowFullId(fullSeqId.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourText(colourTextMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setWrapAlignment(wrapMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void scaleAbove_actionPerformed(ActionEvent e)\r
{\r
viewport.setScaleAboveWrapped(scaleAbove.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void scaleLeft_actionPerformed(ActionEvent e)\r
{\r
viewport.setScaleLeftWrapped(scaleLeft.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void scaleRight_actionPerformed(ActionEvent e)\r
{\r
viewport.setScaleRightWrapped(scaleRight.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowBoxes(viewBoxesMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setShowText(viewTextMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setRenderGaps(renderGapsMenuItem.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
public void sequenceFeatures_actionPerformed(ActionEvent evt)\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
{\r
if (annotationPanelMenuItem.isSelected() &&\r
alignPanel.setAnnotationVisible(annotationPanelMenuItem.isSelected());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void overviewMenuItem_actionPerformed(ActionEvent e)\r
{\r
if (alignPanel.overviewPanel != null)\r
alignPanel.setOverviewPanel(overview);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
{\r
changeColour(null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void clustalColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new ClustalxColourScheme(\r
viewport.alignment.getSequences(), viewport.alignment.getWidth()));\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void zappoColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new ZappoColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void taylorColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new TaylorColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new HydrophobicColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void helixColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new HelixColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void strandColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new StrandColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void turnColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new TurnColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void buriedColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new BuriedColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void nucleotideColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new NucleotideColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
{\r
viewport.setColourAppliesToAllGroups(applyToAllGroups.isSelected());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
if (cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(threshold);\r
+ ( (ResidueColourScheme) cs).setThreshold(threshold,\r
+ viewport.\r
+ getIgnoreGapsConsensus());\r
}\r
else if (cs instanceof ScoreColourScheme)\r
{\r
- ( (ScoreColourScheme) cs).setThreshold(threshold);\r
+ ( (ScoreColourScheme) cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
}\r
\r
viewport.setGlobalColourScheme(cs);\r
}\r
else if (cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) cs).setThreshold(0);\r
+ ( (ResidueColourScheme) cs).setThreshold(0,\r
+ viewport.getIgnoreGapsConsensus());\r
}\r
else if (cs instanceof ScoreColourScheme)\r
{\r
- ( (ScoreColourScheme) cs).setThreshold(0);\r
+ ( (ScoreColourScheme) cs).setThreshold(0, viewport.getIgnoreGapsConsensus());\r
}\r
\r
if (viewport.getConservationSelected())\r
\r
ccs = new ConservationColourScheme(c, cs);\r
\r
- // MUST NOTIFY THE COLOURSCHEME OF CONSENSUS!\r
- ccs.setConsensus(viewport.vconsensus);\r
viewport.setGlobalColourScheme(ccs);\r
\r
ccs.inc = SliderPanel.setConservationSlider(alignPanel, ccs,\r
{\r
if (sg.cs instanceof ResidueColourScheme)\r
{\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
+ ( (ResidueColourScheme) sg.cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
}\r
else if (sg.cs instanceof ScoreColourScheme)\r
{\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold,\r
+ viewport.getIgnoreGapsConsensus());\r
}\r
\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void modifyPID_actionPerformed(ActionEvent e)\r
{\r
if (viewport.getAbovePIDThreshold())\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void modifyConservation_actionPerformed(ActionEvent e)\r
{\r
if (viewport.getConservationSelected())\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
{\r
viewport.setConservationSelected(conservationMenuItem.isSelected());\r
modifyConservation_actionPerformed(null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
{\r
viewport.setAbovePIDThreshold(abovePIDThreshold.isSelected());\r
modifyPID_actionPerformed(null);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- new UserDefinedColours(alignPanel, null);\r
+ if (e.getActionCommand().equals("User Defined..."))\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else\r
+ {\r
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
+ getUserColourSchemes().get(e.getActionCommand());\r
+\r
+ changeColour(udc);\r
+ }\r
}\r
\r
+ public void updateUserColourMenu()\r
+ {\r
+\r
+ Component[] menuItems = colourMenu.getMenuComponents();\r
+ int i, iSize = menuItems.length;\r
+ for (i = 0; i < iSize; i++)\r
+ {\r
+ if (menuItems[i].getName() != null &&\r
+ menuItems[i].getName().equals("USER_DEFINED"))\r
+ {\r
+ colourMenu.remove(menuItems[i]);\r
+ iSize--;\r
+ }\r
+ }\r
+ if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)\r
+ {\r
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
+ getUserColourSchemes().keys();\r
+\r
+ while (userColours.hasMoreElements())\r
+ {\r
+ JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
+ nextElement().toString());\r
+ radioItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ userDefinedColour_actionPerformed(evt);\r
+ }\r
+ });\r
+ colourMenu.insert(radioItem, 15);\r
+ colours.add(radioItem);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void PIDColour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new PIDColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
HistoryItem.SORT));\r
\r
- // AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- AlignmentSorter.sortGroups(viewport.getAlignment());\r
+ AlignmentSorter.sortByGroup(viewport.getAlignment());\r
alignPanel.repaint();\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
{\r
RedundancyPanel sp = new RedundancyPanel(alignPanel, this);\r
100, false);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( (viewport.getSelectionGroup() == null) ||\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void PCAMenuItem_actionPerformed(ActionEvent e)\r
{\r
if ( ( (viewport.getSelectionGroup() != null) &&\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
{\r
NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param type DOCUMENT ME!\r
+ * @param pwType DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ */\r
void NewTreePanel(String type, String pwType, String title)\r
{\r
final TreePanel tp;\r
Desktop.addInternalFrame(tp, title + " from " + this.title, 600, 500);\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param title DOCUMENT ME!\r
+ * @param order DOCUMENT ME!\r
+ */\r
public void addSortByOrderMenuItem(String title, final AlignmentOrder order)\r
{\r
final JMenuItem item = new JMenuItem("by " + title);\r
});\r
}\r
\r
+ /**\r
+ * Maintain the Order by->Displayed Tree menu.\r
+ * Creates a new menu item for a TreePanel with an appropriate\r
+ * <code>jalview.analysis.AlignmentSorter</code> call. Listeners are added\r
+ * to remove the menu item when the treePanel is closed, and adjust\r
+ * the tree leaf to sequence mapping when the alignment is modified.\r
+ * @param treePanel Displayed tree window.\r
+ * @param title SortBy menu item title.\r
+ */\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
{\r
final JMenuItem item = new JMenuItem(title);\r
});\r
}\r
\r
- public void clustalAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
-\r
- if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
- }\r
- else\r
- {\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1)\r
- {\r
- msa = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
- }\r
- }\r
-\r
- if (msa != null)\r
- {\r
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, false, true);\r
- }\r
- }\r
-\r
- public void ClustalRealign_actionPerformed(ActionEvent e)\r
+ /**\r
+ * Work out whether the whole set of sequences\r
+ * or just the selected set will be submitted for multiple alignment.\r
+ *\r
+ */\r
+ private SequenceI[] gatherSequencesForAlignment()\r
{\r
- // TODO:resolve which menu item was actually selected\r
// Now, check we have enough sequences\r
SequenceI[] msa = null;\r
\r
}\r
}\r
}\r
-\r
- if (msa != null)\r
- {\r
- jalview.ws.MsaWSClient ct = new jalview.ws.MsaWSClient("ClustalWS",\r
- title, msa, true, true);\r
- }\r
+ return msa;\r
}\r
\r
- protected void jpred_actionPerformed(ActionEvent e)\r
+ /**\r
+ * Decides what is submitted to a secondary structure prediction service,\r
+ * the currently selected sequence, or the currently selected alignment\r
+ * (where the first sequence in the set is the one that the prediction\r
+ * will be for).\r
+ */\r
+ SequenceI[] gatherSeqOrMsaForSecStrPrediction()\r
{\r
SequenceI seq = null;\r
SequenceI[] msa = null;\r
}\r
}\r
}\r
-\r
if (msa != null)\r
{\r
- JPredClient ct = new JPredClient(title, msa);\r
- }\r
- else if (seq != null)\r
- {\r
- JPredClient ct = new JPredClient(title, seq);\r
- }\r
- else\r
- {\r
- System.err.print(\r
- "JALVIEW ERROR! - Unexpected JPred selection state!\n");\r
- }\r
- }\r
-\r
- protected void msaAlignMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- // TODO:resolve which menu item was actually selected\r
- // Now, check we have enough sequences\r
- SequenceI[] msa = null;\r
-\r
- if ( (viewport.getSelectionGroup() != null) &&\r
- (viewport.getSelectionGroup().getSize() > 1))\r
- {\r
- // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to some common interface!\r
- SequenceGroup seqs = viewport.getSelectionGroup();\r
- int sz;\r
- msa = new SequenceI[sz = seqs.getSize()];\r
-\r
- for (int i = 0; i < sz; i++)\r
- {\r
- msa[i] = (SequenceI) seqs.getSequenceAt(i);\r
- }\r
+ return msa;\r
}\r
else\r
{\r
- Vector seqs = viewport.getAlignment().getSequences();\r
-\r
- if (seqs.size() > 1)\r
+ if (seq != null)\r
{\r
- msa = new SequenceI[seqs.size()];\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- msa[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
+ return new SequenceI[]\r
+ {\r
+ seq};\r
}\r
}\r
-\r
- if (msa != null)\r
- {\r
- MsaWSClient ct = new jalview.ws.MsaWSClient("MuscleWS", title, msa,\r
- false, true);\r
- }\r
+ return null;\r
}\r
-\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
protected void LoadtreeMenuItem_actionPerformed(ActionEvent e)\r
{\r
// Pick the tree file\r
{\r
jalview.io.NewickFile fin = new jalview.io.NewickFile(choice,\r
"File");\r
- viewport.setCurrentTree( ShowNewickTree(fin, choice).getTree() );\r
+ viewport.setCurrentTree(ShowNewickTree(fin, choice).getTree());\r
}\r
catch (Exception ex)\r
{\r
}\r
}\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param nf DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
public TreePanel ShowNewickTree(NewickFile nf, String title)\r
{\r
TreePanel tp = null;\r
+\r
try\r
{\r
nf.parse();\r
+\r
if (nf.getTree() != null)\r
{\r
tp = new TreePanel(viewport,\r
- viewport.getAlignment().getSequences(), nf,\r
- "FromFile",\r
- title);\r
+ viewport.getAlignment().getSequences(), nf,\r
+ "FromFile",\r
+ title);\r
Desktop.addInternalFrame(tp, title, 600, 500);\r
addTreeMenuItem(tp, title);\r
}\r
{\r
ex.printStackTrace();\r
}\r
+\r
return tp;\r
}\r
\r
}\r
}\r
}\r
+\r
+ /**\r
+ * Generates menu items and listener event actions for web service clients\r
+ *\r
+ */\r
+ public void BuildWebServiceMenu()\r
+ {\r
+ if ( (Desktop.discoverer.services != null)\r
+ && (Desktop.discoverer.services.size() > 0))\r
+ {\r
+ Vector msaws = (Vector) Desktop.discoverer.services.get("MsaWS");\r
+ Vector secstrpr = (Vector) Desktop.discoverer.services.get("SecStrPred");\r
+ Vector wsmenu = new Vector();\r
+ if (msaws != null)\r
+ {\r
+ // Add any Multiple Sequence Alignment Services\r
+ final JMenu msawsmenu = new JMenu("Alignment");\r
+ for (int i = 0, j = msaws.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws.\r
+ get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ false, true);\r
+\r
+ }\r
+\r
+ });\r
+ msawsmenu.add(method);\r
+ // Deal with services that we know accept partial alignments.\r
+ if (sh.getName().indexOf("lustal") > -1)\r
+ {\r
+ // We know that ClustalWS can accept partial alignments for refinement.\r
+ final JMenuItem methodR = new JMenuItem(sh.getName()+" Realign");\r
+ methodR.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSequencesForAlignment();\r
+ MsaWSClient ct = new jalview.ws.MsaWSClient(sh, title, msa,\r
+ true, true);\r
+\r
+ }\r
+\r
+ });\r
+ msawsmenu.add(methodR);\r
+\r
+ }\r
+ }\r
+ wsmenu.add(msawsmenu);\r
+ }\r
+ if (secstrpr != null)\r
+ {\r
+ // Add any secondary structure prediction services\r
+ final JMenu secstrmenu = new JMenu("Secondary Structure Prediction");\r
+ for (int i = 0, j = secstrpr.size(); i < j; i++)\r
+ {\r
+ final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle)\r
+ secstrpr.get(i);\r
+ final JMenuItem method = new JMenuItem(sh.getName());\r
+ method.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceI[] msa = gatherSeqOrMsaForSecStrPrediction();\r
+ if (msa.length == 1)\r
+ {\r
+ // Single Sequence prediction\r
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
+ title, msa[0]);\r
+ }\r
+ else\r
+ {\r
+ if (msa.length > 1)\r
+ {\r
+ // Single Sequence prediction\r
+ jalview.ws.JPredClient ct = new jalview.ws.JPredClient(sh,\r
+ title, msa);\r
+ }\r
+ }\r
+ }\r
+ });\r
+ secstrmenu.add(method);\r
+ }\r
+ wsmenu.add(secstrmenu);\r
+ }\r
+ this.webService.removeAll();\r
+ for (int i = 0, j = wsmenu.size(); i < j; i++)\r
+ {\r
+ webService.add( (JMenu) wsmenu.get(i));\r
+ }\r
+ }\r
+ else\r
+ {\r
+ this.webService.removeAll();\r
+ this.webService.add(this.webServiceNoServices);\r
+ }\r
+ // TODO: add in rediscovery function\r
+ // TODO: reduce code redundancy.\r
+ // TODO: group services by location as well as function.\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff