import jalview.jbgui.*;\r
import jalview.schemes.*;\r
import jalview.ws.*;\r
+import javax.swing.event.AncestorEvent;\r
\r
/**\r
* DOCUMENT ME!\r
* @version $Revision$\r
*/\r
public class AlignFrame\r
- extends GAlignFrame\r
+ extends GAlignFrame implements ClipboardOwner\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
+ AlignmentPanel alignPanel;\r
+ AlignViewport viewport;\r
+\r
+ Vector viewports = new Vector();\r
+ Vector alignPanels = new Vector();\r
\r
/** DOCUMENT ME!! */\r
public String currentFileFormat = null;\r
Stack redoList = new Stack();\r
private int treeCount = 0;\r
\r
+\r
/**\r
* Creates a new AlignFrame object.\r
*\r
public AlignFrame(AlignmentI al)\r
{\r
viewport = new AlignViewport(al);\r
+ viewports.add(viewport);\r
+\r
\r
if(viewport.vconsensus==null)\r
{\r
- //Out of memory caluclating consensus.\r
+ //Out of memory calculating consensus.\r
BLOSUM62Colour.setEnabled(false);\r
PIDColour.setEnabled(false);\r
conservationMenuItem.setEnabled(false);\r
}\r
\r
alignPanel = new AlignmentPanel(this, viewport);\r
- alignPanel.annotationPanel.adjustPanelHeight();\r
- alignPanel.annotationSpaceFillerHolder.setPreferredSize(alignPanel.\r
- annotationPanel.getPreferredSize());\r
- alignPanel.annotationScroller.setPreferredSize(alignPanel.annotationPanel.\r
- getPreferredSize());\r
- alignPanel.setAnnotationVisible(viewport.getShowAnnotation());\r
+ alignPanels.add(alignPanel);\r
\r
String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT", "No sort");\r
\r
else if(sortby.equals("Pairwise Identity"))\r
sortPairwiseMenuItem_actionPerformed(null);\r
\r
- getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);\r
+ // remove(tabbedPane);\r
+ getContentPane().add(alignPanel, BorderLayout.CENTER);\r
+\r
+\r
+\r
+ // tabbedPane.add(al.isNucleotide() ? "DNA":"Protein", alignPanel);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+ if(al.getDataset()==null)\r
+ {\r
+ al.setDataset(null);\r
+ }\r
+ // AlignViewport ds = new AlignViewport(al.getDataset(), true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
\r
viewport.addPropertyChangeListener(new PropertyChangeListener()\r
{\r
}\r
});\r
\r
- if(Desktop.desktop!=null)\r
+\r
+ if (Desktop.desktop != null)\r
+ {\r
addServiceListeners();\r
+ setGUINucleotide(al.isNucleotide());\r
+ }\r
}\r
\r
/* Set up intrinsic listeners for dynamically generated GUI bits. */\r
\r
}\r
\r
+ public void setGUINucleotide(boolean nucleotide)\r
+ {\r
+ showTranslation.setVisible( nucleotide );\r
+ sequenceFeatures.setVisible(!nucleotide );\r
+ featureSettings.setVisible( !nucleotide );\r
+ conservationMenuItem.setVisible( !nucleotide );\r
+ modifyConservation.setVisible( !nucleotide );\r
+\r
+ //Deal with separators\r
+ //Remember AlignFrame always starts as protein\r
+ if(nucleotide)\r
+ {\r
+ viewMenu.remove(viewMenu.getItemCount()-2);\r
+ }\r
+ else\r
+ {\r
+ calculateMenu.remove(calculateMenu.getItemCount()-2);\r
+ }\r
+ }\r
+\r
+\r
+ /*\r
+ Added so Castor Mapping file can obtain Jalview Version\r
+ */\r
+ public String getVersion()\r
+ {\r
+ return jalview.bin.Cache.getProperty("VERSION");\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
BufferedReader in = new BufferedReader(new FileReader(file));\r
SequenceI seq = null;\r
- String line, text, token;\r
- UserColourScheme ucs;\r
+ String line, type, desc, token;\r
+\r
int index, start, end;\r
StringTokenizer st;\r
- SequenceGroup sg;\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() != 6)\r
+ if (st.countTokens() == 2)\r
{\r
- System.out.println("Groups file " + file +\r
- " is invalid. Read help file.");\r
- System.exit(1);\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
- text = st.nextToken();\r
+ desc = st.nextToken();\r
token = st.nextToken();\r
if (!token.equals("ID_NOT_SPECIFIED"))\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
+ 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
+\r
+ sf = new SequenceFeature(type, desc, "", start, end);\r
+\r
+ seq.addSequenceFeature(sf);\r
+\r
+\r
+ // sg = new SequenceGroup(text, ucs, true, true, false, start, end);\r
+ // sg.addSequence(seq, false);\r
+\r
+ // viewport.alignment.addGroup(sg);\r
\r
- viewport.alignment.addGroup(sg);\r
}\r
}\r
\r
+ viewport.showSequenceFeatures = true;\r
+\r
+ alignPanel.repaint();\r
+\r
}\r
catch (Exception ex)\r
{\r
}\r
}\r
\r
+ public void fetchSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(this);\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
protected void htmlMenuItem_actionPerformed(ActionEvent e)\r
{\r
- new HTMLOutput(viewport);\r
+ new HTMLOutput(viewport,\r
+ alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),\r
+ alignPanel.seqPanel.seqCanvas.getFeatureRenderer());\r
}\r
\r
public void createImageMap(File file, String image)\r
alignPanel.repaint();\r
}\r
\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
- System.out.println("null here");\r
return;\r
}\r
\r
Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();\r
\r
Hashtable orderedSeqs = new Hashtable();\r
- SequenceI [] seqs = new SequenceI[sg.getSize()];\r
+ SequenceI[] seqs = new SequenceI[sg.getSize()];\r
\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
}\r
}\r
\r
-\r
//FIND START RES\r
//Returns residue following index if gap\r
startRes = seq.findPosition(sg.getStartRes());\r
}\r
\r
seqs[i] = new Sequence(seq.getName(),\r
- seq.getSequence(sg.getStartRes(), sg.getEndRes()+1),\r
+ seq.getSequence(sg.getStartRes(), sg.getEndRes() + 1),\r
startRes,\r
endRes);\r
+ seqs[i].setDescription(seq.getDescription());\r
+ seqs[i].setDBRef(seq.getDBRef());\r
+ seqs[i].setSequenceFeatures(seq.getSequenceFeatures());\r
+ seqs[i].setDatasetSequence(seq.getDatasetSequence());\r
+\r
}\r
\r
- c.setContents(new StringSelection(FastaFile.print(seqs)), null);\r
+ FastaFile ff = new FastaFile();\r
+ ff.addJVSuffix( viewport.showJVSuffix );\r
+ c.setContents(new StringSelection( ff.print(seqs)), this);\r
+ Desktop.jalviewClipboard = new Object[]{seqs, viewport.alignment.getDataset()};\r
}\r
\r
/**\r
}\r
\r
String str = (String) contents.getTransferData(DataFlavor.stringFlavor);\r
+ if(str.length()<1)\r
+ return;\r
\r
String format = IdentifyFile.Identify(str, "Paste");\r
- SequenceI[] sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ SequenceI[] sequences;\r
\r
+ if(Desktop.jalviewClipboard!=null)\r
+ {\r
+ // The clipboard was filled from within Jalview, we must use the sequences\r
+ // And dataset from the copied alignment\r
+ sequences = (SequenceI[])Desktop.jalviewClipboard[0];\r
+ }\r
+ else\r
+ {\r
+ sequences = new FormatAdapter().readFile(str, "Paste", format);\r
+ }\r
\r
if (newAlignment)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+\r
+ Alignment alignment = new Alignment(sequences);\r
+\r
+ if(Desktop.jalviewClipboard!=null)\r
+ alignment.setDataset( (Alignment)Desktop.jalviewClipboard[1] );\r
+ else\r
+ alignment.setDataset( null );\r
+\r
+\r
+ AlignFrame af = new AlignFrame(alignment);\r
String newtitle = new String("Copied sequences");\r
\r
if (title.startsWith("Copied sequences"))\r
{\r
//!newAlignment\r
for (int i = 0; i < sequences.length; i++)\r
- viewport.alignment.addSequence(sequences[i]);\r
+ {\r
+ Sequence newseq = new Sequence(sequences[i].getName(),\r
+ sequences[i].getSequence(), sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ viewport.alignment.addSequence(newseq);\r
+ if(sequences[i].getDatasetSequence()==null)\r
+ {\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ", sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ newseq.setDatasetSequence(ds);\r
+ viewport.alignment.getDataset().addSequence(ds);\r
+ }\r
\r
+ }\r
viewport.setEndSeq(viewport.alignment.getHeight());\r
viewport.alignment.getWidth();\r
viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
alignPanel.annotationPanel.activeRes = null;\r
PaintRefresher.Refresh(null, viewport.alignment);\r
}\r
*\r
* @param e DOCUMENT ME!\r
*/\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ protected void seqLimit_actionPerformed(ActionEvent e)\r
{\r
- viewport.setShowFullId(fullSeqId.isSelected());\r
+ viewport.setShowJVSuffix(seqLimits.isSelected());\r
\r
alignPanel.idPanel.idCanvas.setPreferredSize(alignPanel.calculateIdWidth());\r
alignPanel.repaint();\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
viewport.showSequenceFeatures(sequenceFeatures.isSelected());\r
\r
- if (viewport.showSequenceFeatures &&\r
- ! ( (Alignment) viewport.alignment).featuresAdded)\r
+ if (viewport.showSequenceFeatures)\r
{\r
new SequenceFeatureFetcher(viewport.\r
- alignment,\r
+ alignment,\r
alignPanel);\r
- ( (Alignment) viewport.alignment).featuresAdded = true;\r
}\r
\r
+ featureSettings.setEnabled(true);\r
+\r
alignPanel.repaint();\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- false, true);\r
+ false, true, viewport.getAlignment().getDataset());\r
\r
}\r
\r
{\r
SequenceI[] msa = gatherSequencesForAlignment();\r
new jalview.ws.MsaWSClient(sh, title, msa,\r
- true, true);\r
+ true, true, viewport.getAlignment().getDataset());\r
\r
}\r
\r
// TODO: group services by location as well as function.\r
}\r
\r
+ /* public void vamsasStore_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Export to Vamsas file");\r
+ chooser.setToolTipText("Export");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(viewport);\r
+ //vs.store(chooser.getSelectedFile().getAbsolutePath() );\r
+ vs.storeJalview( chooser.getSelectedFile().getAbsolutePath(), this);\r
+ }\r
+ }*/\r
+\r
+ public void featureSettings_actionPerformed(ActionEvent e)\r
+ {\r
+ new FeatureSettings(viewport, alignPanel);\r
+ }\r
+\r
+\r
+\r
+public void showTranslation_actionPerformed(ActionEvent e)\r
+{\r
+ int s, sSize = viewport.alignment.getHeight();\r
+ SequenceI [] newSeq = new SequenceI[sSize];\r
+\r
+ int res, resSize;\r
+ StringBuffer protein;\r
+ String seq;\r
+ for(s=0; s<sSize; s++)\r
+ {\r
+ protein = new StringBuffer();\r
+ seq = AlignSeq.extractGaps("-. ", viewport.alignment.getSequenceAt(s).getSequence());\r
+ resSize = seq.length();\r
+ for(res = 0; res < resSize; res+=3)\r
+ {\r
+ String codon = seq.substring(res, res+3);\r
+ codon = codon.replace('U', 'T');\r
+ String aa = ResidueProperties.codonTranslate(codon);\r
+ if(aa==null)\r
+ protein.append(viewport.getGapCharacter());\r
+ else if(aa.equals("STOP"))\r
+ protein.append("X");\r
+ else\r
+ protein.append( aa );\r
+ }\r
+ newSeq[s] = new Sequence(viewport.alignment.getSequenceAt(s).getName(), protein.toString());\r
+ }\r
+\r
+\r
+ AlignmentI al = new Alignment(newSeq);\r
+ al.setDataset(null);\r
+\r
+\r
+ ////////////////////////////////\r
+ // Copy annotations across\r
+ jalview.datamodel.AlignmentAnnotation[] annotations\r
+ = viewport.alignment.getAlignmentAnnotation();\r
+ int a, aSize;\r
+ for (int i = 0; i < annotations.length; i++)\r
+ {\r
+\r
+ if (annotations[i].label.equals("Quality") ||\r
+ annotations[i].label.equals("Conservation") ||\r
+ annotations[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+\r
+ aSize = viewport.alignment.getWidth()/3;\r
+ jalview.datamodel.Annotation [] anots =\r
+ new jalview.datamodel.Annotation[aSize];\r
+\r
+ for(a=0; a<viewport.alignment.getWidth(); a++)\r
+ {\r
+ if( annotations[i].annotations[a]==null\r
+ || annotations[i].annotations[a]==null)\r
+ continue;\r
+\r
+ anots[a/3] = new Annotation(\r
+ annotations[i].annotations[a].displayCharacter,\r
+ annotations[i].annotations[a].description,\r
+ annotations[i].annotations[a].secondaryStructure,\r
+ annotations[i].annotations[a].value,\r
+ annotations[i].annotations[a].colour);\r
+ }\r
+\r
+ jalview.datamodel.AlignmentAnnotation aa\r
+ = new jalview.datamodel.AlignmentAnnotation(annotations[i].label,\r
+ annotations[i].description, anots );\r
+ al.addAnnotation(aa);\r
+ }\r
+\r
+\r
+ AlignFrame af = new AlignFrame(al);\r
+ Desktop.addInternalFrame(af, "Translation of "+this.getTitle(),\r
+ NEW_WINDOW_WIDTH,\r
+ NEW_WINDOW_HEIGHT);\r
+\r
+\r
+ // AlignViewport newViewport = new AlignViewport(al);\r
+ // AlignmentPanel ap = new AlignmentPanel(this, newViewport);\r
+ // tabbedPane.add("Protein", ap);\r
+ // viewports.add(newViewport);\r
+ // alignPanels.add(ap);\r
+\r
+ ///Dataset tab\r
+ /////////////////////////\r
+\r
+ // AlignViewport ds = new AlignViewport(al.getDataset());\r
+ // ds.setDataset(true);\r
+ // AlignmentPanel dap = new AlignmentPanel(this, ds);\r
+ // tabbedPane.add("Dataset", dap);\r
+ // viewports.add(ds);\r
+ // alignPanels.add(dap);\r
+ /////////////////////////\r
+\r
+\r
+}\r
+\r
+/*public void tabSelected()\r
+ {\r
+ int index = tabbedPane.getSelectedIndex();\r
+ viewport = (AlignViewport)viewports.elementAt(index);\r
+ alignPanel = (AlignmentPanel)alignPanels.elementAt(index);\r
+ }*/\r
}\r
int endRes;\r
int startSeq;\r
int endSeq;\r
- boolean showFullId = false;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
\r
boolean ignoreGapsInConsensusCalculation = false;\r
\r
+ boolean isDataset = false;\r
+\r
+\r
+ public AlignViewport(AlignmentI al, boolean dataset)\r
+ {\r
+ isDataset = dataset;\r
+ setAlignment(al);\r
+ init();\r
+ }\r
/**\r
* Creates a new AlignViewport object.\r
*\r
public AlignViewport(AlignmentI al)\r
{\r
setAlignment(al);\r
- this.startRes = 0;\r
- this.endRes = al.getWidth() - 1;\r
- this.startSeq = 0;\r
- this.endSeq = al.getHeight() - 1;\r
-\r
- updateFromPreferences();\r
+ init();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void updateFromPreferences()\r
+ void init()\r
{\r
- showFullId = Cache.getDefault("SHOW_FULL_ID", true);\r
+ this.startRes = 0;\r
+ this.endRes = alignment.getWidth() - 1;\r
+ this.startSeq = 0;\r
+ this.endSeq = alignment.getHeight() - 1;\r
+\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
\r
\r
// We must set conservation and consensus before setting colour,\r
// as Blosum and Clustal require this to be done\r
- updateConservation();\r
-\r
- updateConsensus();\r
+ if(vconsensus==null && !isDataset)\r
+ {\r
+ updateConservation();\r
+ updateConsensus();\r
+ }\r
\r
if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
{\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
/**\r
*\r
* @param b DOCUMENT ME!\r
*/\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
{\r
return ignoreGapsInConsensusCalculation;\r
}\r
+\r
+ public void setDataset(boolean b)\r
+ {\r
+ isDataset = b;\r
+ }\r
+\r
+ public boolean isDataset()\r
+ {\r
+ return isDataset;\r
+ }\r
}\r
\r
import jalview.schemes.*;\r
\r
-import org.jibble.epsgraphics.*;\r
-\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.awt.image.*;\r
import java.awt.print.*;\r
\r
import java.io.*;\r
\r
-import javax.imageio.*;\r
-\r
import javax.swing.*;\r
\r
\r
public class AlignmentPanel extends GAlignmentPanel\r
implements AdjustmentListener, Printable\r
{\r
- public AlignViewport av;\r
- OverviewPanel overviewPanel;\r
- SeqPanel seqPanel;\r
- IdPanel idPanel;\r
- IdwidthAdjuster idwidthAdjuster;\r
-\r
- /** DOCUMENT ME!! */\r
- public AlignFrame alignFrame;\r
- ScalePanel scalePanel;\r
- AnnotationPanel annotationPanel;\r
- AnnotationLabels alabels;\r
-\r
- // this value is set false when selection area being dragged\r
- boolean fastPaint = true;\r
- int hextent = 0;\r
- int vextent = 0;\r
-\r
- /**\r
- * Creates a new AlignmentPanel object.\r
- *\r
- * @param af DOCUMENT ME!\r
- * @param av DOCUMENT ME!\r
- */\r
- public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
+ public AlignViewport av;\r
+ OverviewPanel overviewPanel;\r
+ SeqPanel seqPanel;\r
+ IdPanel idPanel;\r
+ IdwidthAdjuster idwidthAdjuster;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public AlignFrame alignFrame;\r
+ ScalePanel scalePanel;\r
+ AnnotationPanel annotationPanel;\r
+ AnnotationLabels alabels;\r
+\r
+ // this value is set false when selection area being dragged\r
+ boolean fastPaint = true;\r
+ int hextent = 0;\r
+ int vextent = 0;\r
+\r
+ /**\r
+ * Creates a new AlignmentPanel object.\r
+ *\r
+ * @param af DOCUMENT ME!\r
+ * @param av DOCUMENT ME!\r
+ */\r
+ public AlignmentPanel(AlignFrame af, final AlignViewport av)\r
+ {\r
+ alignFrame = af;\r
+ this.av = av;\r
+ seqPanel = new SeqPanel(av, this);\r
+ idPanel = new IdPanel(av, this);\r
+\r
+ scalePanel = new ScalePanel(av, this);\r
+\r
+ idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
+ idwidthAdjuster = new IdwidthAdjuster(this);\r
+ idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
+\r
+ annotationPanel = new AnnotationPanel(this);\r
+ alabels = new AnnotationLabels(this);\r
+\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
+ annotationScroller.setViewportView(annotationPanel);\r
+ annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+\r
+ fontChanged();\r
+\r
+ scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
+ seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+\r
+ setScrollValues(0, 0);\r
+\r
+ annotationPanel.adjustPanelHeight();\r
+ annotationSpaceFillerHolder.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ annotationScroller.setPreferredSize(annotationPanel.\r
+ getPreferredSize());\r
+ setAnnotationVisible(av.getShowAnnotation());\r
+\r
+ hscroll.addAdjustmentListener(this);\r
+ vscroll.addAdjustmentListener(this);\r
+\r
+ af.addKeyListener(new KeyAdapter()\r
{\r
- alignFrame = af;\r
- this.av = av;\r
- seqPanel = new SeqPanel(av, this);\r
- idPanel = new IdPanel(av, this);\r
-\r
- scalePanel = new ScalePanel(av, this);\r
-\r
- idPanelHolder.add(idPanel, BorderLayout.CENTER);\r
- idwidthAdjuster = new IdwidthAdjuster(this);\r
- idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ av.setSelectionGroup(null);\r
+ repaint();\r
\r
- annotationPanel = new AnnotationPanel(this);\r
- alabels = new AnnotationLabels(this);\r
+ break;\r
\r
- annotationSpaceFillerHolder.setPreferredSize(annotationPanel.getPreferredSize());\r
- annotationScroller.setPreferredSize(annotationPanel.getPreferredSize());\r
- annotationScroller.setViewportView(annotationPanel);\r
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);\r
+ case KeyEvent.VK_DOWN:\r
+ alignFrame.moveSelectedSequences(false);\r
\r
- fontChanged();\r
+ break;\r
\r
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);\r
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);\r
+ case KeyEvent.VK_UP:\r
+ alignFrame.moveSelectedSequences(true);\r
\r
- setScrollValues(0, 0);\r
+ break;\r
\r
- hscroll.addAdjustmentListener(this);\r
- vscroll.addAdjustmentListener(this);\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ case KeyEvent.VK_DELETE:\r
+ alignFrame.cut_actionPerformed(null);\r
+ break;\r
\r
- af.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- switch (evt.getKeyCode())\r
- {\r
- case 27: // escape key\r
- av.setSelectionGroup(null);\r
- repaint();\r
-\r
- break;\r
-\r
- case KeyEvent.VK_DOWN:\r
- alignFrame.moveSelectedSequences(false);\r
-\r
- break;\r
-\r
- case KeyEvent.VK_UP:\r
- alignFrame.moveSelectedSequences(true);\r
-\r
- break;\r
-\r
- case KeyEvent.VK_BACK_SPACE:\r
- case KeyEvent.VK_DELETE:\r
- alignFrame.cut_actionPerformed(null);\r
- break;\r
-\r
- case KeyEvent.VK_P:\r
- seqPanel.seqCanvas.increaseAARatio();\r
- break;\r
- case KeyEvent.VK_L:\r
- seqPanel.seqCanvas.decreaseAARation();\r
- break;\r
- }\r
- }\r
- });\r
+ case KeyEvent.VK_P:\r
+ seqPanel.seqCanvas.increaseAARatio();\r
+ break;\r
+ case KeyEvent.VK_L:\r
+ seqPanel.seqCanvas.decreaseAARation();\r
+ break;\r
+ }\r
+ }\r
+ });\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void fontChanged()\r
+ {\r
+ // set idCanvas bufferedImage to null\r
+ // to prevent drawing old image\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+\r
+ scalePanelHolder.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
+ av.charHeight + fm.getDescent()));\r
+\r
+ idPanel.idCanvas.gg = null;\r
+ seqPanel.seqCanvas.img = null;\r
+ annotationPanel.adjustPanelHeight();\r
+\r
+ Dimension d = calculateIdWidth();\r
+ d.setSize(d.width + 4, d.height);\r
+ idPanel.idCanvas.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(d);\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
}\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void fontChanged()\r
+ else\r
{\r
- // set idCanvas bufferedImage to null\r
- // to prevent drawing old image\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
-\r
- scalePanelHolder.setPreferredSize(new Dimension(10,\r
- av.charHeight + fm.getDescent()));\r
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10,\r
- av.charHeight + fm.getDescent()));\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
\r
- idPanel.idCanvas.gg = null;\r
- seqPanel.seqCanvas.img = null;\r
- annotationPanel.adjustPanelHeight();\r
+ if (overviewPanel != null)\r
+ overviewPanel.setBoxPosition();\r
\r
- Dimension d = calculateIdWidth();\r
- d.setSize(d.width + 4, d.height);\r
- idPanel.idCanvas.setPreferredSize(d);\r
- hscrollFillerPanel.setPreferredSize(d);\r
+ repaint();\r
+ }\r
\r
- if (av.getWrapAlignment())\r
- {\r
- int max = av.alignment.getWidth() /\r
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
- }\r
- else\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Dimension calculateIdWidth()\r
+ {\r
+ Container c = new Container();\r
\r
- if(overviewPanel!=null)\r
- overviewPanel.setBoxPosition();\r
+ FontMetrics fm = c.getFontMetrics(av.font);\r
+ AlignmentI al = av.getAlignment();\r
\r
- repaint();\r
- }\r
+ int i = 0;\r
+ int idWidth = 0;\r
+ String id;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Dimension calculateIdWidth()\r
+ while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
{\r
- Container c = new Container();\r
+ SequenceI s = al.getSequenceAt(i);\r
\r
- FontMetrics fm = c.getFontMetrics(av.font);\r
- AlignmentI al = av.getAlignment();\r
+ id = s.getDisplayId(av.getShowJVSuffix());\r
\r
- int i = 0;\r
- int idWidth = 0;\r
- String id;\r
-\r
- while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))\r
- {\r
- SequenceI s = al.getSequenceAt(i);\r
+ if (fm.stringWidth(id) > idWidth)\r
+ {\r
+ idWidth = fm.stringWidth(id);\r
+ }\r
\r
- if (av.getShowFullId())\r
- {\r
- id = s.getDisplayId();\r
- }\r
- else\r
- {\r
- id = s.getName();\r
- }\r
+ i++;\r
+ }\r
\r
- if (fm.stringWidth(id) > idWidth)\r
- {\r
- idWidth = fm.stringWidth(id);\r
- }\r
+ // Also check annotation label widths\r
+ i = 0;\r
\r
- i++;\r
- }\r
+ if (al.getAlignmentAnnotation() != null)\r
+ {\r
+ fm = c.getFontMetrics(alabels.getFont());\r
\r
- // Also check annotation label widths\r
- i = 0;\r
+ while (i < al.getAlignmentAnnotation().length)\r
+ {\r
+ String label = al.getAlignmentAnnotation()[i].label;\r
\r
- if (al.getAlignmentAnnotation() != null)\r
+ if (fm.stringWidth(label) > idWidth)\r
{\r
- fm = c.getFontMetrics(alabels.getFont());\r
-\r
- while (i < al.getAlignmentAnnotation().length)\r
- {\r
- String label = al.getAlignmentAnnotation()[i].label;\r
-\r
- if (fm.stringWidth(label) > idWidth)\r
- {\r
- idWidth = fm.stringWidth(label);\r
- }\r
-\r
- i++;\r
- }\r
+ idWidth = fm.stringWidth(label);\r
}\r
\r
- return new Dimension(idWidth, 12);\r
+ i++;\r
+ }\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param results DOCUMENT ME!\r
- */\r
- public void highlightSearchResults(int[] results)\r
- {\r
- seqPanel.seqCanvas.highlightSearchResults(results);\r
+ return new Dimension(idWidth, 12);\r
+ }\r
\r
- // do we need to scroll the panel?\r
- if (results != null)\r
- {\r
- SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
- int start = seq.findIndex(results[1]) - 1;\r
- int end = seq.findIndex(results[2]) - 1;\r
-\r
- if ((av.getStartRes() > start) || (av.getEndRes() < end) ||\r
- ((av.getStartSeq() > results[0]) ||\r
- (av.getEndSeq() < results[0])))\r
- {\r
- setScrollValues(start, results[0]);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public OverviewPanel getOverviewPanel()\r
- {\r
- return overviewPanel;\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param results DOCUMENT ME!\r
+ */\r
+ public void highlightSearchResults(int[] results)\r
+ {\r
+ seqPanel.seqCanvas.highlightSearchResults(results);\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param op DOCUMENT ME!\r
- */\r
- public void setOverviewPanel(OverviewPanel op)\r
+ // do we need to scroll the panel?\r
+ if (results != null)\r
{\r
- overviewPanel = op;\r
- }\r
+ SequenceI seq = av.alignment.getSequenceAt(results[0]);\r
+ int start = seq.findIndex(results[1]) - 1;\r
+ int end = seq.findIndex(results[2]) - 1;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setAnnotationVisible(boolean b)\r
- {\r
- if (!av.wrapAlignment)\r
+ if ( (av.getStartRes() > start) || (av.getEndRes() < end) ||\r
+ ( (av.getStartSeq() > results[0]) ||\r
+ (av.getEndSeq() < results[0])))\r
{\r
- annotationSpaceFillerHolder.setVisible(b);\r
- annotationScroller.setVisible(b);\r
+ setScrollValues(start, results[0]);\r
}\r
- repaint();\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param wrap DOCUMENT ME!\r
- */\r
- public void setWrapAlignment(boolean wrap)\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public OverviewPanel getOverviewPanel()\r
+ {\r
+ return overviewPanel;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param op DOCUMENT ME!\r
+ */\r
+ public void setOverviewPanel(OverviewPanel op)\r
+ {\r
+ overviewPanel = op;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setAnnotationVisible(boolean b)\r
+ {\r
+ if (!av.wrapAlignment)\r
{\r
- av.startSeq = 0;\r
- scalePanelHolder.setVisible(!wrap);\r
- hscroll.setVisible(!wrap);\r
- idwidthAdjuster.setVisible(!wrap);\r
-\r
- if(wrap)\r
- {\r
- annotationScroller.setVisible(false);\r
- annotationSpaceFillerHolder.setVisible(false);\r
- }\r
- else if(av.showAnnotation)\r
- {\r
- annotationScroller.setVisible(true);\r
- annotationSpaceFillerHolder.setVisible(true);\r
- }\r
-\r
- idSpaceFillerPanel1.setVisible(!wrap);\r
-\r
- repaint();\r
+ annotationSpaceFillerHolder.setVisible(b);\r
+ annotationScroller.setVisible(b);\r
}\r
-\r
-\r
- // return value is true if the scroll is valid\r
- public boolean scrollUp(boolean up)\r
+ repaint();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param wrap DOCUMENT ME!\r
+ */\r
+ public void setWrapAlignment(boolean wrap)\r
+ {\r
+ av.startSeq = 0;\r
+ scalePanelHolder.setVisible(!wrap);\r
+ hscroll.setVisible(!wrap);\r
+ idwidthAdjuster.setVisible(!wrap);\r
+\r
+ if (wrap)\r
{\r
- if (up)\r
- {\r
- if (vscroll.getValue() < 1)\r
- {\r
- return false;\r
- }\r
-\r
- fastPaint = false;\r
- vscroll.setValue(vscroll.getValue() - 1);\r
- }\r
- else\r
- {\r
- if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
- {\r
- return false;\r
- }\r
-\r
- fastPaint = false;\r
- vscroll.setValue(vscroll.getValue() + 1);\r
- }\r
-\r
- fastPaint = true;\r
-\r
- return true;\r
+ annotationScroller.setVisible(false);\r
+ annotationSpaceFillerHolder.setVisible(false);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param right DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean scrollRight(boolean right)\r
+ else if (av.showAnnotation)\r
{\r
- if (right)\r
- {\r
- if (hscroll.getValue() < 1)\r
- {\r
- return false;\r
- }\r
+ annotationScroller.setVisible(true);\r
+ annotationSpaceFillerHolder.setVisible(true);\r
+ }\r
\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() - 1);\r
- }\r
- else\r
- {\r
- if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
- {\r
- return false;\r
- }\r
+ idSpaceFillerPanel1.setVisible(!wrap);\r
\r
- fastPaint = false;\r
- hscroll.setValue(hscroll.getValue() + 1);\r
- }\r
+ repaint();\r
+ }\r
\r
- fastPaint = true;\r
+ // return value is true if the scroll is valid\r
+ public boolean scrollUp(boolean up)\r
+ {\r
+ if (up)\r
+ {\r
+ if (vscroll.getValue() < 1)\r
+ {\r
+ return false;\r
+ }\r
\r
- return true;\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() - 1);\r
}\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param x DOCUMENT ME!\r
- * @param y DOCUMENT ME!\r
- */\r
- public void setScrollValues(int x, int y)\r
+ else\r
{\r
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
- 1);\r
-\r
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
-\r
- if (hextent > av.alignment.getWidth())\r
- {\r
- hextent = av.alignment.getWidth();\r
- }\r
-\r
- if (vextent > av.alignment.getHeight())\r
- {\r
- vextent = av.alignment.getHeight();\r
- }\r
-\r
- if ((hextent + x) > av.getAlignment().getWidth())\r
- {\r
- x = av.getAlignment().getWidth() - hextent;\r
- }\r
-\r
- if ((vextent + y) > av.getAlignment().getHeight())\r
- {\r
- y = av.getAlignment().getHeight() - vextent;\r
- }\r
-\r
- if (y < 0)\r
- {\r
- y = 0;\r
- }\r
-\r
- if (x < 0)\r
- {\r
- x = 0;\r
- }\r
+ if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())\r
+ {\r
+ return false;\r
+ }\r
\r
- hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
- vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+ fastPaint = false;\r
+ vscroll.setValue(vscroll.getValue() + 1);\r
}\r
\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param evt DOCUMENT ME!\r
- */\r
- public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ fastPaint = true;\r
+\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param right DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean scrollRight(boolean right)\r
+ {\r
+ if (right)\r
{\r
+ if (hscroll.getValue() < 1)\r
+ {\r
+ return false;\r
+ }\r
\r
- int oldX = av.getStartRes();\r
- int oldY = av.getStartSeq();\r
-\r
- if (evt.getSource() == hscroll)\r
- {\r
- int x = hscroll.getValue();\r
- av.setStartRes(x);\r
- av.setEndRes((x +\r
- (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
- }\r
-\r
- if (evt.getSource() == vscroll)\r
- {\r
- int offy = vscroll.getValue();\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() - 1);\r
+ }\r
+ else\r
+ {\r
+ if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())\r
+ {\r
+ return false;\r
+ }\r
\r
- if (av.getWrapAlignment())\r
- {\r
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- av.setStartRes(vscroll.getValue() * rowSize);\r
- av.setEndRes((vscroll.getValue() + 1) * rowSize);\r
- }\r
- else\r
- {\r
- av.setStartSeq(offy);\r
- av.setEndSeq(offy +\r
- (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
- }\r
- }\r
+ fastPaint = false;\r
+ hscroll.setValue(hscroll.getValue() + 1);\r
+ }\r
\r
- if (overviewPanel != null)\r
- {\r
- overviewPanel.setBoxPosition();\r
- }\r
+ fastPaint = true;\r
\r
- int xShift = av.getStartRes() - oldX;\r
- int yShift = av.getStartSeq() - oldY;\r
+ return true;\r
+ }\r
\r
- if ( (xShift != 0 && yShift != 0) ||\r
- (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
- || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
- || av.getWrapAlignment()\r
- || !fastPaint)\r
- {\r
- // Either no shift at all, or shift greater than visible amount\r
- repaint();\r
- }\r
- else\r
- {\r
- idPanel.idCanvas.fastPaint(yShift);\r
- seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param x DOCUMENT ME!\r
+ * @param y DOCUMENT ME!\r
+ */\r
+ public void setScrollValues(int x, int y)\r
+ {\r
+ av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) -\r
+ 1);\r
\r
- scalePanel.repaint();\r
+ hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;\r
+ vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;\r
\r
- if (av.getShowAnnotation())\r
- {\r
- annotationPanel.fastPaint(xShift);\r
- }\r
- }\r
+ if (hextent > av.alignment.getWidth())\r
+ {\r
+ hextent = av.alignment.getWidth();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param g DOCUMENT ME!\r
- */\r
- public void paintComponent(Graphics g)\r
+ if (vextent > av.alignment.getHeight())\r
{\r
- invalidate();\r
-\r
- Dimension d = idPanel.idCanvas.getPreferredSize();\r
- idPanelHolder.setPreferredSize(d);\r
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
- validate();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- int max = av.alignment.getWidth() / seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());\r
- vscroll.setMaximum(max);\r
- vscroll.setUnitIncrement(1);\r
- vscroll.setVisibleAmount(1);\r
- }\r
- else\r
- {\r
- setScrollValues(av.getStartRes(), av.getStartSeq());\r
- }\r
+ vextent = av.alignment.getHeight();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pg DOCUMENT ME!\r
- * @param pf DOCUMENT ME!\r
- * @param pi DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- *\r
- * @throws PrinterException DOCUMENT ME!\r
- */\r
- public int print(Graphics pg, PageFormat pf, int pi)\r
- throws PrinterException\r
+ if ( (hextent + x) > av.getAlignment().getWidth())\r
{\r
- pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());\r
-\r
- int pwidth = (int) pf.getImageableWidth();\r
- int pheight = (int) pf.getImageableHeight();\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- return printWrappedAlignment(pg, pwidth, pheight, pi);\r
- }\r
- else\r
- {\r
- return printUnwrapped(pg, pwidth, pheight, pi);\r
- }\r
+ x = av.getAlignment().getWidth() - hextent;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pg DOCUMENT ME!\r
- * @param pwidth DOCUMENT ME!\r
- * @param pheight DOCUMENT ME!\r
- * @param pi DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- *\r
- * @throws PrinterException DOCUMENT ME!\r
- */\r
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
- throws PrinterException\r
+ if ( (vextent + y) > av.getAlignment().getHeight())\r
{\r
- int idWidth = calculateIdWidth().width + 4;\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- int scaleHeight = av.charHeight + fm.getDescent();\r
-\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
-\r
- ////////////////////////////////////\r
- /// How many sequences and residues can we fit on a printable page?\r
- int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
-\r
- int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) -\r
- 1;\r
+ y = av.getAlignment().getHeight() - vextent;\r
+ }\r
\r
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
+ if (y < 0)\r
+ {\r
+ y = 0;\r
+ }\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startRes;\r
+ if (x < 0)\r
+ {\r
+ x = 0;\r
+ }\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int endRes;\r
+ hscroll.setValues(x, hextent, 0, av.getAlignment().getWidth());\r
+ vscroll.setValues(y, vextent, 0, av.getAlignment().getHeight());\r
+ }\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int startSeq;\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
\r
- /////////////////////////////\r
- /// Only print these sequences and residues on this page\r
- int endSeq;\r
- startRes = (pi % pagesWide) * totalRes;\r
- endRes = (startRes + totalRes) - 1;\r
+ int oldX = av.getStartRes();\r
+ int oldY = av.getStartSeq();\r
\r
- if (endRes > (av.getAlignment().getWidth() - 1))\r
- {\r
- endRes = av.getAlignment().getWidth() - 1;\r
- }\r
+ if (evt.getSource() == hscroll)\r
+ {\r
+ int x = hscroll.getValue();\r
+ av.setStartRes(x);\r
+ av.setEndRes( (x +\r
+ (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);\r
+ }\r
\r
- startSeq = (pi / pagesWide) * totalSeq;\r
- endSeq = startSeq + totalSeq;\r
+ if (evt.getSource() == vscroll)\r
+ {\r
+ int offy = vscroll.getValue();\r
\r
- if (endSeq > av.getAlignment().getHeight())\r
- {\r
- endSeq = av.getAlignment().getHeight();\r
- }\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.\r
+ seqCanvas.getWidth());\r
+ av.setStartRes(vscroll.getValue() * rowSize);\r
+ av.setEndRes( (vscroll.getValue() + 1) * rowSize);\r
+ }\r
+ else\r
+ {\r
+ av.setStartSeq(offy);\r
+ av.setEndSeq(offy +\r
+ (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));\r
+ }\r
+ }\r
\r
- int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
+ if (overviewPanel != null)\r
+ {\r
+ overviewPanel.setBoxPosition();\r
+ }\r
\r
- if (av.showAnnotation)\r
- {\r
- pagesHigh += annotationPanel.adjustPanelHeight()+3;\r
- }\r
+ int xShift = av.getStartRes() - oldX;\r
+ int yShift = av.getStartSeq() - oldY;\r
\r
- pagesHigh /= pheight;\r
+ if ( (xShift != 0 && yShift != 0) ||\r
+ (Math.abs(xShift) > av.getEndRes() - av.getStartRes()\r
+ || Math.abs(yShift) > av.getEndSeq() - av.getStartSeq())\r
+ || av.getWrapAlignment()\r
+ || !fastPaint)\r
+ {\r
+ // Either no shift at all, or shift greater than visible amount\r
+ repaint();\r
+ }\r
+ else\r
+ {\r
+ idPanel.idCanvas.fastPaint(yShift);\r
+ seqPanel.seqCanvas.fastPaint(xShift, yShift);\r
\r
- if (pi >= (pagesWide * pagesHigh))\r
- {\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
+ scalePanel.repaint();\r
\r
- //draw Scale\r
- pg.translate(idWidth, 0);\r
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
- pg.translate(-idWidth, scaleHeight);\r
+ if (av.getShowAnnotation())\r
+ {\r
+ annotationPanel.fastPaint(xShift);\r
+ }\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ */\r
+ public void paintComponent(Graphics g)\r
+ {\r
+ invalidate();\r
+\r
+ Dimension d = idPanel.idCanvas.getPreferredSize();\r
+ idPanelHolder.setPreferredSize(d);\r
+ hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));\r
+ validate();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ int max = av.alignment.getWidth() /\r
+ seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()) +1;\r
+ vscroll.setMaximum(max);\r
+ vscroll.setUnitIncrement(1);\r
+ vscroll.setVisibleAmount(1);\r
+ }\r
+ else\r
+ {\r
+ setScrollValues(av.getStartRes(), av.getStartSeq());\r
+ }\r
\r
- ////////////////\r
- // Draw the ids\r
- Color currentColor = null;\r
- Color currentTextColor = null;\r
\r
- for (int i = startSeq; i < endSeq; i++)\r
- {\r
- if ((av.getSelectionGroup() != null) &&\r
- av.getSelectionGroup().sequences.contains(\r
- av.getAlignment().getSequenceAt(i)))\r
- {\r
- currentColor = Color.gray;\r
- currentTextColor = Color.black;\r
- }\r
- else\r
- {\r
- currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
- currentTextColor = Color.black;\r
- }\r
+ if( this.getVisibleRect().getBounds() == g.getClipBounds() )\r
+ {\r
+ if (overviewPanel != null)\r
+ overviewPanel.updateOverviewImage();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pf DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int print(Graphics pg, PageFormat pf, int pi)\r
+ throws PrinterException\r
+ {\r
+ pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());\r
+\r
+ int pwidth = (int) pf.getImageableWidth();\r
+ int pheight = (int) pf.getImageableHeight();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ return printWrappedAlignment(pg, pwidth, pheight, pi);\r
+ }\r
+ else\r
+ {\r
+ return printUnwrapped(pg, pwidth, pheight, pi);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)\r
+ throws PrinterException\r
+ {\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
+\r
+ ////////////////////////////////////\r
+ /// How many sequences and residues can we fit on a printable page?\r
+ int totalRes = (pwidth - idWidth) / av.getCharWidth();\r
+\r
+ int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) -\r
+ 1;\r
+\r
+ int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startRes;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endRes;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int startSeq;\r
+\r
+ /////////////////////////////\r
+ /// Only print these sequences and residues on this page\r
+ int endSeq;\r
+ startRes = (pi % pagesWide) * totalRes;\r
+ endRes = (startRes + totalRes) - 1;\r
+\r
+ if (endRes > (av.getAlignment().getWidth() - 1))\r
+ {\r
+ endRes = av.getAlignment().getWidth() - 1;\r
+ }\r
\r
- pg.setColor(currentColor);\r
- pg.fillRect(0, (i-startSeq) * av.charHeight, idWidth,\r
- av.getCharHeight());\r
+ startSeq = (pi / pagesWide) * totalSeq;\r
+ endSeq = startSeq + totalSeq;\r
\r
- pg.setColor(currentTextColor);\r
+ if (endSeq > av.getAlignment().getHeight())\r
+ {\r
+ endSeq = av.getAlignment().getHeight();\r
+ }\r
\r
- String string = av.getAlignment().getSequenceAt(i).getName();\r
+ int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;\r
\r
- if (av.getShowFullId())\r
- {\r
- string = av.getAlignment().getSequenceAt(i).getDisplayId();\r
- }\r
+ if (av.showAnnotation)\r
+ {\r
+ pagesHigh += annotationPanel.adjustPanelHeight() + 3;\r
+ }\r
\r
- pg.drawString(string, 0,\r
- (((i-startSeq) * av.charHeight) + av.getCharHeight()) -\r
- (av.getCharHeight() / 5));\r
- }\r
+ pagesHigh /= pheight;\r
\r
- // draw main sequence panel\r
- pg.translate(idWidth, 0);\r
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
- startRes, startSeq, 0);\r
+ if (pi >= (pagesWide * pagesHigh))\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
\r
- if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
- {\r
- pg.translate(-idWidth, (endSeq - startSeq) * av.charHeight +3);\r
- alabels.drawComponent((Graphics2D) pg, idWidth);\r
- pg.translate(idWidth, 0);\r
- annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes +\r
- 1);\r
- }\r
+ //draw Scale\r
+ pg.translate(idWidth, 0);\r
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);\r
+ pg.translate( -idWidth, scaleHeight);\r
\r
- return Printable.PAGE_EXISTS;\r
- }\r
+ ////////////////\r
+ // Draw the ids\r
+ Color currentColor = null;\r
+ Color currentTextColor = null;\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param pg DOCUMENT ME!\r
- * @param pwidth DOCUMENT ME!\r
- * @param pheight DOCUMENT ME!\r
- * @param pi DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- *\r
- * @throws PrinterException DOCUMENT ME!\r
- */\r
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
- int pi) throws PrinterException\r
+ for (int i = startSeq; i < endSeq; i++)\r
{\r
-\r
- int annotationHeight = 0;\r
- AnnotationLabels labels = null;\r
- if (av.showAnnotation)\r
+ if ( (av.getSelectionGroup() != null) &&\r
+ av.getSelectionGroup().sequences.contains(\r
+ av.getAlignment().getSequenceAt(i)))\r
{\r
- annotationHeight = annotationPanel.adjustPanelHeight();\r
- labels = new AnnotationLabels(av);\r
+ currentColor = Color.gray;\r
+ currentTextColor = Color.black;\r
+ }\r
+ else\r
+ {\r
+ currentColor = av.getAlignment().getSequenceAt(i).getColor();\r
+ currentTextColor = Color.black;\r
}\r
\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap\r
- + annotationHeight;\r
-\r
-\r
- int idWidth = calculateIdWidth().width + 4;\r
-\r
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
- idWidth);\r
+ pg.setColor(currentColor);\r
+ pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,\r
+ av.getCharHeight());\r
\r
- int totalHeight = cHeight * (av.alignment.getWidth() / resWidth +1);\r
+ pg.setColor(currentTextColor);\r
\r
- pg.setColor(Color.white);\r
- pg.fillRect(0, 0, pwidth, pheight);\r
- pg.setFont(av.getFont());\r
+ String string = av.getAlignment().getSequenceAt(i).getDisplayId\r
+ ( av.getShowJVSuffix());\r
\r
+ pg.drawString(string, 0,\r
+ ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) -\r
+ (av.getCharHeight() / 5));\r
+ }\r
\r
- ////////////////\r
- // Draw the ids\r
- pg.setColor(Color.black);\r
+ // draw main sequence panel\r
+ pg.translate(idWidth, 0);\r
+ seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq,\r
+ startRes, startSeq, 0);\r
\r
- pg.translate(0, -pi * pheight);\r
+ if (av.showAnnotation && (endSeq == av.alignment.getHeight()))\r
+ {\r
+ pg.translate( -idWidth, (endSeq - startSeq) * av.charHeight + 3);\r
+ alabels.drawComponent( (Graphics2D) pg, idWidth);\r
+ pg.translate(idWidth, 0);\r
+ annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +\r
+ 1);\r
+ }\r
\r
- pg.setClip(0, pi * pheight, pwidth, pheight);\r
+ return Printable.PAGE_EXISTS;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param pg DOCUMENT ME!\r
+ * @param pwidth DOCUMENT ME!\r
+ * @param pheight DOCUMENT ME!\r
+ * @param pi DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ *\r
+ * @throws PrinterException DOCUMENT ME!\r
+ */\r
+ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,\r
+ int pi)\r
+ throws PrinterException\r
+ {\r
+\r
+ int annotationHeight = 0;\r
+ AnnotationLabels labels = null;\r
+ if (av.showAnnotation)\r
+ {\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
+ labels = new AnnotationLabels(av);\r
+ }\r
\r
- int ypos = hgap;\r
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
- av.getFont().getSize());\r
- pg.setFont(italic);\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
\r
- do\r
- {\r
- for (int i = 0; i < av.alignment.getHeight(); i++)\r
- {\r
- SequenceI s = av.alignment.getSequenceAt(i);\r
- String string = s.getName();\r
+ int idWidth = calculateIdWidth().width + 4;\r
\r
- if (av.getShowFullId())\r
- {\r
- string = s.getDisplayId();\r
- }\r
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -\r
+ idWidth);\r
\r
- pg.drawString(string, 0,\r
- ( (i * av.charHeight) + ypos + av.charHeight) -\r
- (av.charHeight / 5));\r
- }\r
- if (labels != null)\r
- {\r
- pg.translate(0,\r
- ypos +\r
- (av.getAlignment().getHeight() * av.charHeight));\r
-\r
- pg.setFont(av.getFont());\r
- labels.drawComponent( pg, idWidth );\r
- pg.setFont(italic);\r
- pg.translate(0,\r
- -ypos -\r
- (av.getAlignment().getHeight() * av.charHeight));\r
- }\r
+ int totalHeight = cHeight * (av.alignment.getWidth() / resWidth + 1);\r
\r
- ypos += cHeight;\r
- }\r
- while (ypos < totalHeight);\r
+ pg.setColor(Color.white);\r
+ pg.fillRect(0, 0, pwidth, pheight);\r
+ pg.setFont(av.getFont());\r
\r
- pg.translate(idWidth, 0);\r
+ ////////////////\r
+ // Draw the ids\r
+ pg.setColor(Color.black);\r
\r
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
+ pg.translate(0, -pi * pheight);\r
\r
- if ((pi * pheight) < totalHeight)\r
- {\r
- return Printable.PAGE_EXISTS;\r
+ pg.setClip(0, pi * pheight, pwidth, pheight);\r
\r
- }\r
- else\r
- {\r
- return Printable.NO_SUCH_PAGE;\r
- }\r
- }\r
+ int ypos = hgap;\r
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC,\r
+ av.getFont().getSize());\r
+ pg.setFont(italic);\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makeEPS(File epsFile)\r
+ do\r
{\r
- boolean accurateText = true;\r
-\r
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time");\r
-\r
- // If we need to prompt, and if the GUI is visible then\r
- // Prompt for EPS rendering style\r
- if (renderStyle.equalsIgnoreCase("Prompt each time")\r
- && !\r
- (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true")))\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
{\r
- EPSOptions eps = new EPSOptions();\r
- renderStyle = eps.getValue();\r
-\r
- if(eps.cancelled || renderStyle==null)\r
- return;\r
+ SequenceI s = av.alignment.getSequenceAt(i);\r
+ String string = s.getDisplayId( av.getShowJVSuffix());\r
\r
- renderStyle = eps.getValue();\r
+ pg.drawString(string, 0,\r
+ ( (i * av.charHeight) + ypos + av.charHeight) -\r
+ (av.charHeight / 5));\r
}\r
-\r
- if (renderStyle.equalsIgnoreCase("text"))\r
+ if (labels != null)\r
{\r
- accurateText = false;\r
- }\r
-\r
+ pg.translate(0,\r
+ ypos +\r
+ (av.getAlignment().getHeight() * av.charHeight));\r
\r
- if(epsFile == null)\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.\r
- JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"eps"},\r
- new String[]\r
- {"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from alignment");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- epsFile = chooser.getSelectedFile();\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
- }\r
-\r
-\r
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
-\r
-\r
- if (av.getWrapAlignment())\r
- {\r
- height = getWrappedHeight();\r
- width = seqPanel.getWidth() + idPanel.getWidth();\r
- }\r
- else if (av.getShowAnnotation())\r
- {\r
- height += annotationPanel.adjustPanelHeight()+3;\r
- }\r
+ pg.setFont(av.getFont());\r
+ labels.drawComponent(pg, idWidth);\r
+ pg.setFont(italic);\r
+ pg.translate(0,\r
+ -ypos -\r
+ (av.getAlignment().getHeight() * av.charHeight));\r
+ }\r
\r
+ ypos += cHeight;\r
+ }\r
+ while (ypos < totalHeight);\r
\r
- try\r
- {\r
- FileOutputStream out = new FileOutputStream(epsFile);\r
- EpsGraphics2D pg = new EpsGraphics2D("Example", out, 0, 0, width,\r
- height);\r
+ pg.translate(idWidth, 0);\r
\r
- pg.setAccurateTextMode(accurateText);\r
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);\r
\r
- if (av.getWrapAlignment())\r
- {\r
- printWrappedAlignment(pg, width, height, 0);\r
- }\r
- else\r
- {\r
- printUnwrapped(pg, width, height, 0);\r
- }\r
+ if ( (pi * pheight) < totalHeight)\r
+ {\r
+ return Printable.PAGE_EXISTS;\r
\r
- pg.flush();\r
- pg.close();\r
- }\r
- catch (OutOfMemoryError err)\r
- {\r
- System.out.println("########################\n"\r
- + "OUT OF MEMORY " + epsFile + "\n"\r
- + "########################");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of memory creating EPS file!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("Create EPS: " + err);\r
- System.gc();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
}\r
+ else\r
+ {\r
+ return Printable.NO_SUCH_PAGE;\r
+ }\r
+ }\r
\r
+ void makeAlignmentImage(int type, File file)\r
+ {\r
+ int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
+ int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
\r
- public void makePNGImageMap(File imgMapFile, String imageName)\r
+ if (av.getWrapAlignment())\r
{\r
- ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
- //////////////////////////////////////////////\r
- int idWidth = calculateIdWidth().width + 4;\r
- FontMetrics fm = getFontMetrics(av.getFont());\r
- int scaleHeight = av.charHeight + fm.getDescent();\r
-\r
- // Gen image map\r
- //////////////////////////////////\r
- if(imgMapFile!=null)\r
- {\r
- try\r
- {\r
- PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
- out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
- out.println("<img src=\"" + imageName +\r
- "\" border=\"0\" usemap=\"#Map\" >"\r
- +"<map name=\"Map\">");\r
-\r
- for (int s = 0; s < av.alignment.getHeight(); s++)\r
- {\r
- SequenceI seq = av.alignment.getSequenceAt(s);\r
- SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- int sy = s * av.charHeight + scaleHeight;\r
- for (int res = groups[i].getStartRes();\r
- res < groups[i].getEndRes() + 1; res++)\r
- {\r
- int alIndex = seq.findPosition(res);\r
- Object obj = ResidueProperties.aa2Triplet.get(\r
- seq.getCharAt(res) + "");\r
- if (obj == null)\r
- continue;\r
-\r
- String triplet = obj.toString();\r
-\r
- out.println(\r
- "<area shape=\"rect\" coords=\""\r
- + (idWidth + res * av.charWidth) + ","\r
- + sy + ","\r
- + (idWidth + (res + 1) * av.charWidth) + ","\r
- + (av.charHeight + sy) + "\""\r
- + " onMouseOver=\"toolTip('"\r
- + alIndex + " " + triplet +\r
- "<br><em>" + groups[i].getName() +\r
- "</em>')\"; onMouseOut=\"toolTip()\"; "\r
- + " href=\"#\">");\r
- }\r
- }\r
- }\r
-\r
- out.println("</map></body></html>");\r
- out.close();\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }///////////END OF IMAGE MAP\r
-\r
+ height = getWrappedHeight();\r
+ width = seqPanel.getWidth() + idPanel.getWidth();\r
}\r
-\r
- int getWrappedHeight()\r
+ else if (av.getShowAnnotation())\r
{\r
+ height += annotationPanel.adjustPanelHeight() + 3;\r
+ }\r
\r
- int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
- seqPanel.seqCanvas.getWidth());\r
-\r
- int hgap = av.charHeight;\r
- if (av.scaleAboveWrapped)\r
- hgap += av.charHeight;\r
-\r
- int annotationHeight = 0;\r
- if (av.showAnnotation)\r
+ jalview.util.ImageMaker im;\r
+ if(type==jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Create PNG image from alignment",\r
+ width, height, file, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Create EPS file from alignment",\r
+ width, height, file, alignFrame.getTitle() );\r
+\r
+ try\r
+ {\r
+ if (av.getWrapAlignment())\r
{\r
- annotationHeight = annotationPanel.adjustPanelHeight();\r
+ if(im.getGraphics()!=null)\r
+ printWrappedAlignment(im.getGraphics(), width, height, 0);\r
+ }\r
+ else\r
+ {\r
+ if(im.getGraphics()!=null)\r
+ printUnwrapped(im.getGraphics(), width, height, 0);\r
}\r
\r
- int cHeight = av.getAlignment().getHeight() * av.charHeight\r
- + hgap\r
- + annotationHeight;\r
-\r
-\r
- int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
-\r
- return height;\r
+ im.writeImage();\r
}\r
+ catch (OutOfMemoryError err)\r
+ {\r
+ System.out.println("########################\n"\r
+ + "OUT OF MEMORY " + file + "\n"\r
+ + "########################");\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of Memory Creating Image!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ System.out.println("Create IMAGE: " + err);\r
+ System.gc();\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void makePNG(File pngFile)\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makeEPS(File epsFile)\r
+ {\r
+ makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void makePNG(File pngFile)\r
+ {\r
+ makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);\r
+ }\r
+\r
+ public void makePNGImageMap(File imgMapFile, String imageName)\r
+ {\r
+ ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS\r
+ //////////////////////////////////////////////\r
+ int idWidth = calculateIdWidth().width + 4;\r
+ FontMetrics fm = getFontMetrics(av.getFont());\r
+ int scaleHeight = av.charHeight + fm.getDescent();\r
+\r
+ // Gen image map\r
+ //////////////////////////////////\r
+ if (imgMapFile != null)\r
{\r
- if(pngFile==null)\r
+ try\r
{\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.\r
- JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"png"},\r
- new String[]\r
- {"Portable network graphics"},\r
- "Portable network graphics");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from alignment");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
+ PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));\r
+ out.println(jalview.io.HTMLOutput.getImageMapHTML());\r
+ out.println("<img src=\"" + imageName +\r
+ "\" border=\"0\" usemap=\"#Map\" >"\r
+ + "<map name=\"Map\">");\r
+\r
+ for (int s = 0; s < av.alignment.getHeight(); s++)\r
{\r
- return;\r
+ SequenceI seq = av.alignment.getSequenceAt(s);\r
+ SequenceGroup[] groups = av.alignment.findAllGroups(seq);\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ int sy = s * av.charHeight + scaleHeight;\r
+ for (int res = groups[i].getStartRes();\r
+ res < groups[i].getEndRes() + 1; res++)\r
+ {\r
+ int alIndex = seq.findPosition(res);\r
+ Object obj = ResidueProperties.aa2Triplet.get(\r
+ seq.getCharAt(res) + "");\r
+ if (obj == null)\r
+ continue;\r
+\r
+ String triplet = obj.toString();\r
+\r
+ out.println(\r
+ "<area shape=\"rect\" coords=\""\r
+ + (idWidth + res * av.charWidth) + ","\r
+ + sy + ","\r
+ + (idWidth + (res + 1) * av.charWidth) + ","\r
+ + (av.charHeight + sy) + "\""\r
+ + " onMouseOver=\"toolTip('"\r
+ + alIndex + " " + triplet +\r
+ "<br><em>" + groups[i].getName() +\r
+ "</em>')\"; onMouseOut=\"toolTip()\"; "\r
+ + " href=\"#\">");\r
+ }\r
+ }\r
}\r
\r
- pngFile = chooser.getSelectedFile();\r
+ out.println("</map></body></html>");\r
+ out.close();\r
\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
}\r
-\r
-\r
-\r
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight) + 30;\r
- int width = idPanel.getWidth() + (av.alignment.getWidth() * av.charWidth);\r
-\r
- if (av.getWrapAlignment())\r
+ catch (Exception ex)\r
{\r
- height = getWrappedHeight();\r
- width = seqPanel.getWidth() + idPanel.getWidth();\r
+ ex.printStackTrace();\r
}\r
- else if (av.getShowAnnotation())\r
- {\r
- height += annotationPanel.adjustPanelHeight()+3;\r
- }\r
+ } ///////////END OF IMAGE MAP\r
\r
- try\r
- {\r
+ }\r
\r
- FileOutputStream out = new FileOutputStream(pngFile);\r
+ int getWrappedHeight()\r
+ {\r
\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics2D png = (Graphics2D) bi.getGraphics();\r
+ int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(\r
+ seqPanel.seqCanvas.getWidth());\r
\r
- png.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
+ int hgap = av.charHeight;\r
+ if (av.scaleAboveWrapped)\r
+ hgap += av.charHeight;\r
\r
- if (av.getWrapAlignment())\r
- {\r
- printWrappedAlignment(png, width, height, 0);\r
- }\r
- else\r
- {\r
- printUnwrapped(png, width, height, 0);\r
- }\r
+ int annotationHeight = 0;\r
+ if (av.showAnnotation)\r
+ {\r
+ annotationHeight = annotationPanel.adjustPanelHeight();\r
+ }\r
\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (OutOfMemoryError err)\r
- {\r
- System.out.println("########################\n"\r
- + "OUT OF MEMORY " + pngFile + "\n"\r
- + "########################");\r
-\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Out of memory creating PNG!!"\r
- +\r
- "\nSee help files for increasing Java Virtual Machine memory."\r
- , "Out of memory",\r
- JOptionPane.WARNING_MESSAGE);\r
- System.out.println("Create PNG: " + err);\r
- System.gc();\r
+ int cHeight = av.getAlignment().getHeight() * av.charHeight\r
+ + hgap\r
+ + annotationHeight;\r
\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-}\r
+ int height = ( (av.alignment.getWidth() / chunkWidth) + 1) * cHeight;\r
\r
+ return height;\r
+ }\r
\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class Preview extends JFrame\r
-{\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class Preview\r
+ extends JFrame\r
+ {\r
/**\r
* Creates a new Preview object.\r
*\r
*/\r
public Preview(Image image)\r
{\r
- setResizable(true);\r
- setSize(image.getWidth(this), image.getHeight(this));\r
- setVisible(true);\r
- getContentPane().setLayout(new BorderLayout());\r
- getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
- validate();\r
- repaint();\r
+ setResizable(true);\r
+ setSize(image.getWidth(this), image.getHeight(this));\r
+ setVisible(true);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(new PreviewPanel(image), BorderLayout.CENTER);\r
+ validate();\r
+ repaint();\r
}\r
-}\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-class PreviewPanel extends JPanel\r
-{\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+ class PreviewPanel\r
+ extends JPanel\r
+ {\r
Image image;\r
\r
/**\r
*/\r
public PreviewPanel(Image image)\r
{\r
- this.image = image;\r
+ this.image = image;\r
}\r
\r
/**\r
*/\r
public void paintComponent(Graphics g)\r
{\r
- if (image != null)\r
- {\r
- g.drawImage(image, 0, 0, this);\r
- }\r
- else\r
- {\r
- System.out.println("DEBUG:image is null");\r
- }\r
+ if (image != null)\r
+ {\r
+ g.drawImage(image, 0, 0, this);\r
+ }\r
+ else\r
+ {\r
+ System.out.println("DEBUG:image is null");\r
+ }\r
}\r
+ }\r
}\r
textarea.setText(text);\r
}\r
\r
+ public void appendText(String text)\r
+ {\r
+ textarea.append(text);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
static final int xOffset = 30;
static final int yOffset = 30;
public static jalview.ws.Discoverer discoverer;
+
+ public static Object [] jalviewClipboard;
+
+
/**
* Creates a new Desktop object.
*/
{
Image image = null;
+
try
{
java.net.URL url = getClass().getResource("/images/logo.gif");
{
}
- setTitle("Jalview 2005");
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
desktop = new JDesktopPane();
desktop.setBackground(Color.white);
{}
}
+
/**
* DOCUMENT ME!
*
*/
public void aboutMenuItem_actionPerformed(ActionEvent e)
{
- StringBuffer message = new StringBuffer("JalView 2005 version " +
+ StringBuffer message = new StringBuffer("JalView version " +
jalview.bin.Cache.getProperty(
"VERSION") +
"; last updated: " +
}
}
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+ getProperty("LAST_DIRECTORY"));
+
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Load Vamsas file");
+ chooser.setToolTipText("Import");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);
+ vs.load(
+ chooser.getSelectedFile().getAbsolutePath()
+ );
+ }
+
+ }*/
+
+
+ public void inputSequence_actionPerformed(ActionEvent e)
+ {
+ SequenceFetcher sf = new SequenceFetcher(null);
+ }
}
extends JPanel\r
{\r
JDialog dialog;\r
- boolean cancelled = false;\r
+ public boolean cancelled = false;\r
String value;\r
\r
public EPSOptions()\r
\r
import java.util.*;\r
\r
+import java.awt.image.*;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
public class FeatureRenderer\r
{\r
AlignViewport av;\r
- SequenceGroup currentSequenceGroup = null;\r
- SequenceGroup[] allGroups = null;\r
Color resBoxColour;\r
- Graphics graphics;\r
+ float transparency = 1.0f;\r
+ FontMetrics fm;\r
+ int charOffset;\r
+ boolean drawText = true;\r
+\r
+ // The following vector holds the features which are\r
+ // to be added, in the correct order or rendering\r
+ Vector featuresDisplayed = null;\r
\r
/**\r
* Creates a new FeatureRenderer object.\r
public FeatureRenderer(AlignViewport av)\r
{\r
this.av = av;\r
+ initColours();\r
+ }\r
+\r
+ /**\r
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\r
+ */\r
+ BufferedImage bi;\r
+ public synchronized Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ if(!av.showSequenceFeatures)\r
+ return initialCol;\r
+\r
+ if (bi == null)\r
+ bi = new BufferedImage(1, 1, BufferedImage.TYPE_INT_RGB);\r
+\r
+ bi.setRGB(0,0, initialCol.getRGB());\r
+\r
+ drawText = false;\r
+\r
+ drawSequence(bi.getGraphics(), seq, i, i, 0, 0, 1, 1);\r
+ drawText = true;\r
+\r
+ return new Color(bi.getRGB(0, 0));\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param width DOCUMENT ME!\r
* @param height DOCUMENT ME!\r
*/\r
- public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
- int start, int end, int x1, int y1, int width, int height)\r
+ public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int x1, int y1, int width, int height)\r
{\r
- Vector features = seq.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
\r
- while (e.hasMoreElements())\r
+//System.out.println(start+" "+end+" "+x1+" "+y1);\r
+ if (seq.getDatasetSequence().getSequenceFeatures() == null\r
+ || seq.getDatasetSequence().getSequenceFeatures().size()==0)\r
+ return;\r
+\r
+ fm = g.getFontMetrics();\r
+\r
+ if (transparency != 1)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, transparency));\r
+ }\r
+\r
+ String type;\r
+ SequenceFeature sf;\r
+ if (featuresDisplayed == null)\r
+ findAllFeatures();\r
+\r
+ Enumeration e = featuresDisplayed.elements(), e2;\r
+\r
+ // Loop through each visible feature\r
+ while (e.hasMoreElements())\r
+ {\r
+\r
+ type = e.nextElement().toString();\r
+ e2 = seq.getDatasetSequence().getSequenceFeatures().elements();\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ while (e2.hasMoreElements())\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
\r
- if (sf.getStart() > seq.getEnd())\r
- {\r
- continue;\r
- }\r
+ sf = (SequenceFeature) e2.nextElement();\r
+ if (!type.equals(sf.getType()))\r
+ continue;\r
+\r
+ if (sf.getBegin() > seq.getEnd())\r
+ continue;\r
+\r
+ if (type.equals("disulfide bond"))\r
+ {\r
+\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+\r
+ }\r
+ else\r
+ renderFeature(g, seq,\r
+ seq.findIndex(sf.getBegin()) - 1,\r
+ seq.findIndex(sf.getEnd()) - 1,\r
+ type, start, end, x1, y1, width, height);\r
+ }\r
+ }\r
+\r
+ if(transparency!=1.0f)\r
+ {\r
+ Graphics2D g2 = (Graphics2D) g;\r
+ g2.setComposite(\r
+ AlphaComposite.getInstance(\r
+ AlphaComposite.SRC_OVER, 1.0f));\r
+ }\r
+ }\r
+\r
\r
- int fstart = seq.findIndex(sf.getStart()) - 1;\r
- int fend = seq.findIndex(sf.getEnd()) - 1;\r
+ void renderFeature(Graphics g, SequenceI seq,\r
+ int fstart, int fend, String type, int start, int end, int x1, int y1, int width, int height)\r
+ {\r
+\r
+ if (((fstart <= end) && (fend >= start)))\r
+ {\r
+ if (fstart < start)\r
+ { // fix for if the feature we have starts before the sequence start,\r
+ fstart = start; // but the feature end is still valid!!\r
+ }\r
\r
- if (((fstart <= end) && (fend >= start)))\r
+ if (fend >= end)\r
+ {\r
+ fend = end;\r
+ }\r
+ for (int i = fstart; i <= fend; i++)\r
+ {\r
+ char s = seq.getSequence().charAt(i);\r
+\r
+ if (jalview.util.Comparison.isGap(s))\r
{\r
- if (fstart < start)\r
- { // fix for if the feature we have starts before the sequence start,\r
- fstart = start; // but the feature end is still valid!!\r
- }\r
-\r
- if (fend >= end)\r
- {\r
- fend = end;\r
- }\r
-\r
- if (fstart == fend)\r
- {\r
- g.setColor(Color.red);\r
- g.fillRoundRect((fstart - start) * width, y1, width,\r
- height, 4, 4);\r
- g.setColor(Color.white);\r
-\r
- char s = seq.getSequence().charAt(fstart);\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + (width * (fstart - start)),\r
- (y1 + height) - pady);\r
- }\r
- else\r
- {\r
- for (int i = fstart; i <= fend; i++)\r
- {\r
- char s = seq.getSequence().charAt(i);\r
-\r
- if (jalview.util.Comparison.isGap(s))\r
- {\r
- continue;\r
- }\r
-\r
- g.setColor(Color.blue);\r
- g.fillRect((i - start) * width, y1, width, height);\r
-\r
- g.setColor(Color.white);\r
-\r
- FontMetrics fm = g.getFontMetrics();\r
- int charOffset = (width - fm.charWidth(s)) / 2;\r
- int pady = height / 5;\r
- g.drawString(String.valueOf(s),\r
- charOffset + x1 + (width * (i - start)),\r
- (y1 + height) - pady);\r
- }\r
- }\r
+ continue;\r
}\r
+\r
+ g.setColor(getColour(type));\r
+\r
+ g.fillRect( (i - start) * width, y1, width, height);\r
+\r
+ if(drawText)\r
+ {\r
+ g.setColor(Color.white);\r
+ charOffset = (width - fm.charWidth(s)) / 2;\r
+ g.drawString(String.valueOf(s),\r
+ charOffset + x1 + (width * (i - start)),\r
+ (y1 + height) - height / 5); //pady = height / 5;\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ void findAllFeatures()\r
+ {\r
+ Vector features = new Vector();\r
+ SequenceFeature sf;\r
+ featuresDisplayed = new Vector();\r
+ Enumeration e;\r
+ for (int i = 0; i < av.alignment.getHeight(); i++)\r
+ {\r
+ features = av.alignment.getSequenceAt(i).getDatasetSequence().\r
+ getSequenceFeatures();\r
+ if (features == null)\r
+ continue;\r
+\r
+ e = features.elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature) e.nextElement();\r
+ if (!featuresDisplayed.contains(sf.getType()))\r
+ {\r
+ featuresDisplayed.addElement(sf.getType());\r
+ }\r
}\r
+ }\r
+ }\r
+\r
+ public Color getColour(String featureType)\r
+ {\r
+ return (Color)featureColours.get(featureType);\r
}\r
+\r
+ public void setColour(String featureType, Color col)\r
+ {\r
+ featureColours.put(featureType, col);\r
+ }\r
+\r
+ public void setTransparency(float value)\r
+ {\r
+ transparency = value;\r
+ }\r
+\r
+ public float getTransparency()\r
+ {\r
+ return transparency;\r
+ }\r
+\r
+ public void setFeaturePriority(Object [][] data)\r
+ {\r
+ // The feature table will display high priority\r
+ // features at the top, but theses are the ones\r
+ // we need to render last, so invert the data\r
+ featuresDisplayed.clear();\r
+ for(int i=data.length-1; i>-1; i--)\r
+ {\r
+ String type = data[i][0].toString();\r
+ setColour(type, (Color)data[i][1]);\r
+ if( ((Boolean)data[i][2]).booleanValue() )\r
+ featuresDisplayed.addElement(type);\r
+ }\r
+ }\r
+\r
+ Hashtable featureColours = new Hashtable();\r
+ void initColours()\r
+ {\r
+ featureColours.put("active site", new Color(255, 75, 0));\r
+ featureColours.put("binding site", new Color(245, 85, 0));\r
+ featureColours.put("calcium-binding region", new Color(235, 95, 0));\r
+ featureColours.put("chain", new Color(225, 105, 0));\r
+ featureColours.put("coiled-coil region", new Color(215, 115, 0));\r
+ featureColours.put("compositionally biased region", new Color(205, 125, 0));\r
+ featureColours.put("cross-link", new Color(195, 135, 0));\r
+ featureColours.put("disulfide bond", new Color(230,230,0));\r
+ featureColours.put("DNA-binding region", new Color(175, 155, 0));\r
+ featureColours.put("domain", new Color(165, 165, 0));\r
+ featureColours.put("glycosylation site", new Color(155, 175, 0));\r
+ featureColours.put("helix", new Color(145, 185, 0));\r
+ featureColours.put("initiator methionine", new Color(135, 195, 5));\r
+ featureColours.put("lipid moiety-binding region", new Color(125, 205, 15));\r
+ featureColours.put("metal ion-binding site", new Color(115, 215, 25));\r
+ featureColours.put("modified residue", new Color(105, 225, 35));\r
+ featureColours.put("mutagenesis site", new Color(95, 235, 45));\r
+ featureColours.put("non-consecutive residues", new Color(85, 245, 55));\r
+ featureColours.put("non-terminal residue", new Color(75, 255, 65));\r
+ featureColours.put("nucleotide phosphate-binding region",new Color(65, 245, 75));\r
+ featureColours.put("peptide", new Color(55, 235, 85));\r
+ featureColours.put("propeptide", new Color(45, 225, 95));\r
+ featureColours.put("region of interest", new Color(35, 215, 105));\r
+ featureColours.put("repeat", new Color(25, 205, 115));\r
+ featureColours.put("selenocysteine", new Color(15, 195, 125));\r
+ featureColours.put("sequence conflict", new Color(5, 185, 135));\r
+ featureColours.put("sequence variant", new Color(0, 175, 145));\r
+ featureColours.put("short sequence motif", new Color(0, 165, 155));\r
+ featureColours.put("signal peptide", new Color(0, 155, 165));\r
+ featureColours.put("site", new Color(0, 145, 175));\r
+ featureColours.put("splice variant", new Color(0, 135, 185));\r
+ featureColours.put("strand", new Color(0, 125, 195));\r
+ featureColours.put("topological domain", new Color(0, 115, 205));\r
+ featureColours.put("transit peptide", new Color(0, 105, 215));\r
+ featureColours.put("transmembrane region", new Color(0, 95, 225));\r
+ featureColours.put("turn", new Color(0, 85, 235));\r
+ featureColours.put("unsure residue", new Color(0, 75, 245));\r
+ featureColours.put("zinc finger region", new Color(0, 65, 255));\r
+ }\r
+\r
}\r
--- /dev/null
+package jalview.gui;\r
+\r
+import jalview.datamodel.*;\r
+import javax.swing.*;\r
+import javax.swing.event.*;\r
+import java.awt.*;\r
+import java.util.*;\r
+import javax.swing.BorderFactory;\r
+import java.awt.event.*;\r
+import javax.swing.table.*;\r
+import java.io.*;\r
+import jalview.io.JalviewFileChooser;\r
+\r
+public class FeatureSettings extends JPanel\r
+{\r
+\r
+ final FeatureRenderer fr;\r
+ final AlignmentPanel ap;\r
+ final AlignViewport av;\r
+ Object [][] originalData;\r
+ final JInternalFrame frame;\r
+ JScrollPane scrollPane = new JScrollPane();\r
+ JTable table;\r
+\r
+ public FeatureSettings(AlignViewport av, final AlignmentPanel ap)\r
+ {\r
+ this.ap = ap;\r
+ this.av = av;\r
+ fr = ap.seqPanel.seqCanvas.getFeatureRenderer();\r
+ av.alignment.getSequences();\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ Desktop.addInternalFrame(frame, "Sequence Feature Settings", 400, 300);\r
+\r
+ setTableData();\r
+\r
+ final JSlider transparency = new JSlider(0, 70, 0);\r
+ transparency.addChangeListener(new ChangeListener()\r
+ {\r
+ public void stateChanged(ChangeEvent evt)\r
+ {\r
+ fr.setTransparency( (float) (100 - transparency.getValue()) / 100f);\r
+ ap.repaint();\r
+ }\r
+ });\r
+\r
+ JPanel transPanel = new JPanel(new FlowLayout());\r
+ transPanel.add(new JLabel("Transparency"));\r
+ transPanel.add(transparency);\r
+\r
+ //////////////////////////////////////////////\r
+ //We're going to need those OK cancel buttons\r
+ JPanel buttonPanel = new JPanel(new FlowLayout());\r
+ JButton button = new JButton("OK");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception exe)\r
+ {}\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+ button = new JButton("Cancel");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ try\r
+ {\r
+ updateFeatureRenderer(originalData);\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception exe)\r
+ {}\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+\r
+ button = new JButton("Load Colours");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ load();\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+ button = new JButton("Save Colours");\r
+ button.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ save();\r
+ }\r
+ });\r
+ buttonPanel.add(button);\r
+\r
+ this.setLayout(new BorderLayout());\r
+ JPanel bigPanel = new JPanel(new BorderLayout());\r
+ bigPanel.add(transPanel, BorderLayout.SOUTH);\r
+ bigPanel.add(scrollPane, BorderLayout.CENTER);\r
+\r
+ add(bigPanel, BorderLayout.CENTER);\r
+ add(buttonPanel, BorderLayout.SOUTH);\r
+\r
+\r
+ }\r
+\r
+ void setTableData()\r
+ {\r
+ Vector allFeatures = new Vector();\r
+ Vector features;\r
+ Enumeration e;\r
+ SequenceFeature sf;\r
+\r
+ for(int i=0; i< av.alignment.getHeight(); i++)\r
+ {\r
+ features = av.alignment.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ if(features==null)\r
+ continue;\r
+\r
+ e = features.elements();\r
+ while(e.hasMoreElements())\r
+ {\r
+ sf = (SequenceFeature)e.nextElement();\r
+ if(!allFeatures.contains(sf.getType()))\r
+ {\r
+ allFeatures.addElement(sf.getType());\r
+ }\r
+ }\r
+ }\r
+ if(allFeatures.size()<1)\r
+ {\r
+ try{\r
+ frame.setClosed(true);\r
+ }catch(Exception ex){}\r
+ return;\r
+ }\r
+\r
+ int fSize = allFeatures.size();\r
+\r
+ String type;\r
+ boolean originalExists = false;\r
+ if(originalData!=null)\r
+ originalExists = true;\r
+ else\r
+ originalData = new Object[fSize][3];\r
+\r
+ Object [][] data = new Object[fSize][3];\r
+ for(int i=0; i<fSize; i++)\r
+ {\r
+ type = allFeatures.elementAt(i).toString();\r
+ Color col = fr.getColour(type);\r
+ data[i][0]=type;\r
+ data[i][1]=col;\r
+ if(fr.featuresDisplayed!=null)\r
+ data[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
+ else\r
+ data[i][2] = new Boolean(true);\r
+\r
+ if(!originalExists)\r
+ {\r
+ originalData[i][0] = type;\r
+ originalData[i][1] = col;\r
+ if (fr.featuresDisplayed != null)\r
+ originalData[i][2] = new Boolean(fr.featuresDisplayed.contains(type));\r
+ else\r
+ originalData[i][2] = new Boolean(true);\r
+ }\r
+ }\r
+ ////////////////////////////////////\r
+ //Now build the table\r
+ table = new JTable(new FeatureTableModel(data));\r
+ scrollPane.setViewportView(table);\r
+ table.getTableHeader().setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setFont(new Font("Verdana", Font.PLAIN, 12));\r
+ table.setDefaultRenderer(Color.class,\r
+ new ColorRenderer());\r
+\r
+ table.setDefaultEditor(Color.class,\r
+ new ColorEditor());\r
+\r
+ table.getColumnModel().getColumn(0).setPreferredWidth(200);\r
+\r
+ table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);\r
+\r
+ table.addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ selectedRow = table.rowAtPoint(evt.getPoint());\r
+ }\r
+ });\r
+\r
+ table.addMouseMotionListener(new MouseMotionAdapter()\r
+ {\r
+ public void mouseDragged(MouseEvent evt)\r
+ {\r
+ int newRow = table.rowAtPoint(evt.getPoint());\r
+ if(newRow!=selectedRow\r
+ && selectedRow!=-1\r
+ && newRow!=-1)\r
+ {\r
+ Object[] temp = new Object[3];\r
+ temp[0] = table.getValueAt(selectedRow, 0);\r
+ temp[1] = table.getValueAt(selectedRow, 1);\r
+ temp[2] = table.getValueAt(selectedRow, 2);\r
+\r
+ table.setValueAt(table.getValueAt(newRow, 0), selectedRow, 0);\r
+ table.setValueAt(table.getValueAt(newRow, 1), selectedRow, 1);\r
+ table.setValueAt(table.getValueAt(newRow, 2), selectedRow, 2);\r
+\r
+ table.setValueAt(temp[0], newRow, 0);\r
+ table.setValueAt(temp[1], newRow, 1);\r
+ table.setValueAt(temp[2], newRow, 2);\r
+\r
+ selectedRow = newRow;\r
+ }\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+ void load()\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "fc" },\r
+ new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Load Feature Colours");\r
+ chooser.setToolTipText("Load");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ File file = chooser.getSelectedFile();\r
+\r
+ try\r
+ {\r
+ InputStreamReader in = new InputStreamReader(new FileInputStream(\r
+ file), "UTF-8");\r
+\r
+ jalview.binding.JalviewUserColours jucs = new jalview.binding.\r
+ JalviewUserColours();\r
+ jucs = (jalview.binding.JalviewUserColours) jucs.unmarshal(in);\r
+\r
+\r
+ for (int i = 0; i < jucs.getColourCount(); i++)\r
+ {\r
+ fr.setColour( jucs.getColour(i).getName(),\r
+ new Color(Integer.parseInt( jucs.getColour(i).getRGB(), 16)));\r
+ }\r
+\r
+ setTableData();\r
+ ap.repaint();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ System.out.println("Error loading User ColourFile\n" + ex);\r
+ }\r
+ }\r
+ }\r
+\r
+ void save()\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "fc" },\r
+ new String[] { "Sequence Feature Colours" }, "Sequence Feature Colours");\r
+ chooser.setFileView(new jalview.io.JalviewFileView());\r
+ chooser.setDialogTitle("Save Feature Colour Scheme");\r
+ chooser.setToolTipText("Save");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.binding.JalviewUserColours ucs = new jalview.binding.JalviewUserColours();\r
+ ucs.setSchemeName("Sequence Features");\r
+ try\r
+ {\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(\r
+ new FileOutputStream(choice), "UTF-8"));\r
+\r
+ Enumeration e = fr.featureColours.keys();\r
+ while(e.hasMoreElements())\r
+ {\r
+\r
+\r
+ jalview.binding.Colour col = new jalview.binding.Colour();\r
+ col.setName(e.nextElement().toString());\r
+ col.setRGB(jalview.util.Format.getHexString(\r
+ fr.getColour(col.getName())));\r
+ ucs.addColour(col);\r
+ }\r
+\r
+ ucs.marshal(out);\r
+ out.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ }\r
+\r
+ public void updateFeatureRenderer(Object [][] data)\r
+ {\r
+ fr.setFeaturePriority( data );\r
+ ap.repaint();\r
+ }\r
+\r
+ int selectedRow =-1;\r
+\r
+\r
+ /////////////////////////////////////////////////////////////////////////\r
+ // http://java.sun.com/docs/books/tutorial/uiswing/components/table.html\r
+ /////////////////////////////////////////////////////////////////////////\r
+ class FeatureTableModel\r
+ extends AbstractTableModel\r
+ {\r
+ FeatureTableModel(Object[][] data)\r
+ {\r
+ this.data = data;\r
+ }\r
+\r
+ private String[] columnNames = {"Feature Type", "Colour","Display"};\r
+ private Object[][] data;\r
+\r
+ public Object[][] getData()\r
+ {\r
+ return data;\r
+ }\r
+\r
+ public int getColumnCount() {\r
+ return columnNames.length;\r
+ }\r
+\r
+ public Object[] getRow(int row)\r
+ {\r
+ return data[row];\r
+ }\r
+\r
+ public int getRowCount() {\r
+ return data.length;\r
+ }\r
+\r
+ public String getColumnName(int col) {\r
+ return columnNames[col];\r
+ }\r
+\r
+ public Object getValueAt(int row, int col) {\r
+ return data[row][col];\r
+ }\r
+\r
+ public Class getColumnClass(int c) {\r
+ return getValueAt(0, c).getClass();\r
+ }\r
+\r
+ public boolean isCellEditable(int row, int col) {\r
+ return col==0 ? false:true;\r
+ }\r
+\r
+ public void setValueAt(Object value, int row, int col) {\r
+ data[row][col] = value;\r
+ fireTableCellUpdated(row, col);\r
+ updateFeatureRenderer(data);\r
+ }\r
+\r
+ }\r
+ class ColorRenderer extends JLabel\r
+ implements TableCellRenderer {\r
+ javax.swing.border.Border unselectedBorder = null;\r
+ javax.swing.border.Border selectedBorder = null;\r
+\r
+ public ColorRenderer() {\r
+ setOpaque(true); //MUST do this for background to show up.\r
+ }\r
+\r
+ public Component getTableCellRendererComponent(\r
+ JTable table, Object color,\r
+ boolean isSelected, boolean hasFocus,\r
+ int row, int column) {\r
+ Color newColor = (Color)color;\r
+ setBackground(newColor);\r
+ if (isSelected) {\r
+ if (selectedBorder == null) {\r
+ selectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
+ table.getSelectionBackground());\r
+ }\r
+ setBorder(selectedBorder);\r
+ } else {\r
+ if (unselectedBorder == null) {\r
+ unselectedBorder = BorderFactory.createMatteBorder(2,5,2,5,\r
+ table.getBackground());\r
+ }\r
+ setBorder(unselectedBorder);\r
+ }\r
+\r
+ setToolTipText("RGB value: " + newColor.getRed() + ", "\r
+ + newColor.getGreen() + ", "\r
+ + newColor.getBlue());\r
+ return this;\r
+ }\r
+ }\r
+}\r
+\r
+ class ColorEditor extends AbstractCellEditor\r
+ implements TableCellEditor,\r
+ ActionListener {\r
+ Color currentColor;\r
+ JButton button;\r
+ JColorChooser colorChooser;\r
+ JDialog dialog;\r
+ protected static final String EDIT = "edit";\r
+\r
+ public ColorEditor() {\r
+ //Set up the editor (from the table's point of view),\r
+ //which is a button.\r
+ //This button brings up the color chooser dialog,\r
+ //which is the editor from the user's point of view.\r
+ button = new JButton();\r
+ button.setActionCommand(EDIT);\r
+ button.addActionListener(this);\r
+ button.setBorderPainted(false);\r
+ //Set up the dialog that the button brings up.\r
+ colorChooser = new JColorChooser();\r
+ dialog = JColorChooser.createDialog(button,\r
+ "Select new Colour",\r
+ true, //modal\r
+ colorChooser,\r
+ this, //OK button handler\r
+ null); //no CANCEL button handler\r
+ }\r
+\r
+ /**\r
+ * Handles events from the editor button and from\r
+ * the dialog's OK button.\r
+ */\r
+ public void actionPerformed(ActionEvent e) {\r
+\r
+ if (EDIT.equals(e.getActionCommand())) {\r
+ //The user has clicked the cell, so\r
+ //bring up the dialog.\r
+ button.setBackground(currentColor);\r
+ colorChooser.setColor(currentColor);\r
+ dialog.setVisible(true);\r
+\r
+ //Make the renderer reappear.\r
+ fireEditingStopped();\r
+\r
+ } else { //User pressed dialog's "OK" button.\r
+ currentColor = colorChooser.getColor();\r
+ }\r
+ }\r
+\r
+ //Implement the one CellEditor method that AbstractCellEditor doesn't.\r
+ public Object getCellEditorValue() {\r
+ return currentColor;\r
+ }\r
+\r
+ //Implement the one method defined by TableCellEditor.\r
+ public Component getTableCellEditorComponent(JTable table,\r
+ Object value,\r
+ boolean isSelected,\r
+ int row,\r
+ int column) {\r
+ currentColor = (Color)value;\r
+ return button;\r
+ }\r
+}\r
fontName.addItem(fonts[i]);\r
}\r
\r
- for (int i = 1; i < 31; i++)\r
+ for (int i = 1; i < 51; i++)\r
{\r
fontSize.addItem(i + "");\r
}\r
--- /dev/null
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+\r
+public class GFeatureSelector\r
+ extends JPanel\r
+{\r
+ public GFeatureSelector()\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ jLabel1.setText("Feature");\r
+ this.add(jLabel1);\r
+ }\r
+\r
+ JLabel jLabel1 = new JLabel();\r
+}\r
gg.setColor(Color.black);\r
}\r
\r
- String string = s.getName();\r
\r
- if (av.getShowFullId())\r
- {\r
- string = s.getDisplayId();\r
- }\r
-\r
- gg.drawString(string, 0,\r
- (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
+ gg.drawString( s.getDisplayId(av.getShowJVSuffix()),\r
+ 0, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5));\r
}\r
\r
/**\r
\r
gg.setColor(currentTextColor);\r
\r
- String string = av.alignment.getSequenceAt(i).getName();\r
-\r
- if (av.getShowFullId())\r
- {\r
- string = av.alignment.getSequenceAt(i).getDisplayId();\r
- }\r
+ String string = av.alignment.getSequenceAt(i).getDisplayId( av.getShowJVSuffix());\r
\r
gg.drawString(string, 0,\r
(((i - starty) * av.charHeight) + av.charHeight) -\r
add(idCanvas, BorderLayout.CENTER);\r
addMouseListener(this);\r
addMouseMotionListener(this);\r
+ ToolTipManager.sharedInstance().registerComponent(this);\r
}\r
\r
/**\r
*/\r
public void mouseMoved(MouseEvent e)\r
{\r
+ int y = e.getY();\r
+\r
+ if (av.getWrapAlignment())\r
+ {\r
+ y = getWrappedY(y);\r
+ }\r
+\r
+ int seq = av.getIndex(y);\r
+ if(seq!=-1)\r
+ {\r
+ StringBuffer tip = new StringBuffer("<html>");\r
+ tip.append(av.alignment.getSequenceAt(seq).getDisplayId(true));\r
+ if (av.alignment.getSequenceAt(seq).getDescription() != null)\r
+ {\r
+ tip.append("<table width=250 border=0><tr><td><i>");\r
+ tip.append(av.alignment.getSequenceAt(seq).getDescription());\r
+ tip.append("</i></td></tr></table>");\r
+ }\r
+ tip.append("</html>");\r
+ setToolTipText(tip.toString());\r
+ }\r
+\r
}\r
\r
int getWrappedY(int y)\r
*/\r
public void mouseClicked(MouseEvent e)\r
{\r
- if (e.getClickCount() < 2)\r
+ if (e.getClickCount() < 2)\r
return;\r
\r
java.util.Vector links = Preferences.sequenceURLLinks;\r
//DEFAULT LINK IS FIRST IN THE LINK LIST\r
int seq = av.getIndex(y);\r
String id = av.getAlignment().getSequenceAt(seq).getName();\r
+ if (id.indexOf("|") > -1)\r
+ id = id.substring(id.lastIndexOf("|") + 1);\r
+\r
\r
String url = links.elementAt(0).toString();\r
url = url.substring(url.indexOf("|")+1);\r
*/\r
void selectSeqs(int start, int end)\r
{\r
+ if(av.getSelectionGroup()==null)\r
+ return;\r
+\r
lastid = start;\r
\r
if (end < start)\r
\r
for (int i = start; i <= end; i++)\r
{\r
- av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),\r
+ av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),\r
true);\r
}\r
}\r
import java.net.*;\r
\r
import java.util.*;\r
+\r
import java.util.jar.*;\r
\r
import javax.swing.*;\r
\r
jseq.setId(id);\r
\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
+ {\r
+ Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements();\r
+ while(en.hasMoreElements())\r
+ {\r
+ Features features = new Features();\r
+ jalview.datamodel.SequenceFeature sf\r
+ = (jalview.datamodel.SequenceFeature)en.nextElement();\r
+\r
+ features.setBegin(sf.getBegin());\r
+ features.setEnd(sf.getEnd());\r
+ features.setDescription(sf.getDescription());\r
+ features.setStatus(sf.getStatus());\r
+ features.setType(sf.getType());\r
+ jseq.addFeatures(features);\r
+ }\r
+ }\r
+\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
+ {\r
+ Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
+ while(en.hasMoreElements())\r
+ {\r
+ Pdbids pdb = new Pdbids();\r
+ jalview.datamodel.PDBEntry entry\r
+ = (jalview.datamodel.PDBEntry)en.nextElement();\r
+\r
+ pdb.setId(entry.getId());\r
+ pdb.setType(entry.getType());\r
+\r
+ if(entry.getProperty()!=null)\r
+ {\r
+ PdbentryItem item = new PdbentryItem();\r
+ Hashtable properties = entry.getProperty();\r
+ Enumeration en2 = properties.keys();\r
+ while(en2.hasMoreElements())\r
+ {\r
+ Property prop = new Property();\r
+ String key = en2.nextElement().toString();\r
+ prop.setName(key);\r
+ prop.setValue( properties.get(key).toString() );\r
+ item.addProperty(prop);\r
+ }\r
+ pdb.addPdbentryItem(item);\r
+ }\r
+\r
+ jseq.addPdbids(pdb);\r
+ }\r
+ }\r
+\r
jms.addJSeq(jseq);\r
vamsasSet.addSequence(vamsasSeq);\r
id++;\r
jms.setJGroup(groups);\r
}\r
\r
+\r
///////////SAVE VIEWPORT\r
Viewport view = new Viewport();\r
view.setTitle(af.getTitle());\r
view.setShowBoxes(av.getShowBoxes());\r
view.setShowColourText(av.getColourText());\r
view.setShowConservation(av.showConservation);\r
- view.setShowFullId(av.getShowFullId());\r
+ view.setShowFullId(av.getShowJVSuffix());\r
view.setShowIdentity(av.showIdentity);\r
view.setShowQuality(av.showQuality);\r
view.setShowSequenceFeatures(av.showSequenceFeatures);\r
view.setShowText(av.getShowText());\r
view.setWrapAlignment(av.getWrapAlignment());\r
\r
+ if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)\r
+ {\r
+ jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();\r
+\r
+ Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();\r
+ while (e.hasMoreElements())\r
+ {\r
+ String type = e.nextElement().toString();\r
+ Setting setting = new Setting();\r
+ setting.setType(type);\r
+ setting.setColour(\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB()\r
+ );\r
+ setting.setDisplay(\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type)\r
+ );\r
+\r
+ fs.addSetting(setting);\r
+\r
+ }\r
+ jms.setFeatureSettings(fs);\r
+\r
+ }\r
+\r
jms.addViewport(view);\r
\r
+\r
object.setJalviewModelSequence(jms);\r
object.getVamsasModel().addSequenceSet(vamsasSet);\r
\r
//LOAD SEQUENCES\r
jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
-\r
for (int i = 0; i < vamsasSeq.length; i++)\r
{\r
jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
seqids.add(jseqs[i]);\r
}\r
\r
+ ///SequenceFeatures are added to the DatasetSequence,\r
+ // so we must create the dataset before loading features\r
/////////////////////////////////\r
jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+ al.setDataset(null);\r
+ /////////////////////////////////\r
\r
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ if (JSEQ[i].getFeaturesCount() > 0)\r
+ {\r
+ Features[] features = JSEQ[i].getFeatures();\r
+ for (int f = 0; f < features.length; f++)\r
+ {\r
+ //features[f].getBegin()\r
+ jalview.datamodel.SequenceFeature sf\r
+ = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
+ features[f].getDescription(), features[f].getStatus(),\r
+ features[f].getBegin(), features[f].getEnd());\r
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
+ }\r
+ }\r
+ if (JSEQ[i].getPdbidsCount() > 0)\r
+ {\r
+ Pdbids[] ids = JSEQ[i].getPdbids();\r
+ for (int p = 0; p < ids.length; p++)\r
+ {\r
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
+ entry.setId(ids[p].getId());\r
+ entry.setType(ids[p].getType());\r
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
+ }\r
+\r
+ }\r
+ }\r
/////////////////////////////////\r
//////////////////////////////////\r
//LOAD ANNOTATIONS\r
\r
AlignFrame af = new AlignFrame(al);\r
\r
+\r
// af.changeColour() );\r
/////////////////////////\r
//LOAD GROUPS\r
af.viewport.setConservationSelected(view.getConservationSelected());\r
af.conservationMenuItem.setSelected(view.getConservationSelected());\r
\r
- af.viewport.setShowFullId(view.getShowFullId());\r
- af.fullSeqId.setSelected(view.getShowFullId());\r
+ af.viewport.setShowJVSuffix(view.getShowFullId());\r
+ af.seqLimits.setSelected(view.getShowFullId());\r
\r
af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
view.getFontStyle(), view.getFontSize()));\r
\r
if (view.getShowSequenceFeatures())\r
{\r
- af.viewport.showSequenceFeatures = true;\r
- af.sequenceFeatures.setSelected(true);\r
- new SequenceFeatureFetcher(al, af.alignPanel);\r
- al.featuresAdded = true;\r
+ af.featureSettings.setEnabled(true);\r
+ af.viewport.showSequenceFeatures = true;\r
+ af.sequenceFeatures.setSelected(true);\r
+ }\r
+\r
+ if(jms.getFeatureSettings()!=null)\r
+ {\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector();\r
+ // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null)\r
+ // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();\r
+ for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
+ {\r
+ Setting setting = jms.getFeatureSettings().getSetting(fs);\r
+\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
+ new java.awt.Color(setting.getColour()));\r
+ if(setting.getDisplay())\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.addElement(setting.getType());\r
+ }\r
}\r
\r
Desktop.addInternalFrame(af, view.getTitle(),\r
\r
// Can set different properties in this seqCanvas than\r
// main visible SeqCanvas\r
- SeqCanvas overviewSeq;\r
+ SequenceRenderer sr;\r
+ FeatureRenderer fr;\r
\r
/**\r
* Creates a new OverviewPanel object.\r
this.ap = ap;\r
setLayout(null);\r
\r
- overviewSeq = new SeqCanvas(av);\r
- overviewSeq.isOverview = true;\r
- overviewSeq.sr.renderGaps = false;\r
+ sr = new SequenceRenderer(av);\r
+ sr.renderGaps( false );\r
+ fr = new FeatureRenderer(av);\r
+ fr.transparency = ap.seqPanel.seqCanvas.getFeatureRenderer().transparency;\r
+ fr.featuresDisplayed = ap.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed;\r
\r
// scale the initial size of overviewpanel to shape of alignment\r
float initialScale = (float) av.alignment.getWidth() / (float) av.alignment.getHeight();\r
\r
- if(av.vconsensus==null)\r
+ if(av.conservation==null)\r
graphHeight = 0;\r
\r
\r
\r
\r
Graphics mg = miniMe.getGraphics();\r
+ mg.setColor(Color.orange);\r
+ mg.fillRect(0,0,width, miniMe.getHeight());\r
\r
float sampleCol = (float) alwidth / (float) width;\r
float sampleRow = (float) alheight / (float) sequencesHeight;\r
\r
+ int lastcol=-1, lastrow=-1;\r
+ Color color = Color.white;\r
for (int col = 0; col < width; col++)\r
{\r
for (int row = 0; row < sequencesHeight; row++)\r
{\r
- overviewSeq.drawPanel(mg,\r
- (int) (col * sampleCol),\r
- (int) (col * sampleCol),\r
- (int) (row * sampleRow),\r
- (int) (row * sampleRow) + 1,\r
- (int) (col * sampleCol),\r
- (int) (row * sampleRow), 0);\r
- mg.translate(0, 1);\r
+ if((int)(col*sampleCol) == lastcol && (int)(row*sampleRow)==lastrow)\r
+ {\r
+ miniMe.setRGB(col,row,color.getRGB());\r
+ continue;\r
+ }\r
+\r
+ lastrow = (int)(row*sampleRow);\r
+ lastcol = (int)(col*sampleCol);\r
+\r
+ color = sr.getResidueBoxColour(\r
+ av.alignment.getSequenceAt(lastrow), lastcol);\r
+\r
+ if(av.showSequenceFeatures)\r
+ {\r
+ color = fr.findFeatureColour(color,\r
+ av.alignment.getSequenceAt(lastrow),\r
+ lastcol);\r
+ }\r
+\r
+ miniMe.setRGB(col,row,color.getRGB());\r
\r
if (av.conservation != null)\r
+ {\r
+ mg.translate(col, sequencesHeight);\r
ap.annotationPanel.drawGraph(mg, av.conservation,\r
(int) (sampleCol) + 1,\r
graphHeight,\r
(int) (col * sampleCol),\r
(int) (col * sampleCol) + 1);\r
-\r
+ mg.translate(-col, -sequencesHeight);\r
+ }\r
}\r
- mg.translate(0, -sequencesHeight);\r
- mg.translate(1, 0);\r
-\r
}\r
\r
System.gc();\r
\r
import java.util.*;\r
import javax.swing.*;\r
-import java.io.FileOutputStream;\r
-import org.jibble.epsgraphics.EpsGraphics2D;\r
-import javax.imageio.ImageIO;\r
-import java.awt.image.BufferedImage;\r
import java.awt.print.*;\r
\r
\r
\r
\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
*/\r
public void eps_actionPerformed(ActionEvent e)\r
{\r
- boolean accurateText = true;\r
-\r
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",\r
- "Prompt each time");\r
-\r
- // If we need to prompt, and if the GUI is visible then\r
- // Prompt for EPS rendering style\r
- if (renderStyle.equalsIgnoreCase("Prompt each time")\r
- && !\r
- (System.getProperty("java.awt.headless") != null\r
- && System.getProperty("java.awt.headless").equals("true")))\r
- {\r
- EPSOptions eps = new EPSOptions();\r
- renderStyle = eps.getValue();\r
-\r
- if (renderStyle == null || eps.cancelled)\r
- return;\r
-\r
- }\r
-\r
- if (renderStyle.equalsIgnoreCase("text"))\r
- {\r
- accurateText = false;\r
- }\r
-\r
- int width = rc.getWidth();\r
- int height = rc.getHeight();\r
-\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"eps"},\r
- new String[]\r
- {"Encapsulated Postscript"},\r
- "Encapsulated Postscript");\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create EPS file from PCA");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
-\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
- EpsGraphics2D pg = new EpsGraphics2D("PCA", out, 0, 0, width,\r
- height);\r
-\r
- pg.setAccurateTextMode(accurateText);\r
-\r
- rc.drawBackground(pg, rc.bgColour);\r
- rc.drawScene(pg);\r
-\r
- if (rc.drawAxes == true)\r
- {\r
- rc.drawAxes(pg);\r
- }\r
-\r
-\r
- pg.flush();\r
- pg.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ makePCAImage(jalview.util.ImageMaker.EPS);\r
}\r
\r
/**\r
*/\r
public void png_actionPerformed(ActionEvent e)\r
{\r
+ makePCAImage(jalview.util.ImageMaker.PNG);\r
+ }\r
+\r
+ void makePCAImage(int type)\r
+ {\r
int width = rc.getWidth();\r
int height = rc.getHeight();\r
\r
- try\r
- {\r
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(\r
- jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"), new String[]\r
- {"png"},\r
- new String[]\r
- {"Portable network graphics"},\r
- "Portable network graphics");\r
-\r
- chooser.setFileView(new jalview.io.JalviewFileView());\r
- chooser.setDialogTitle("Create PNG image from PCA");\r
- chooser.setToolTipText("Save");\r
-\r
- int value = chooser.showSaveDialog(this);\r
+ jalview.util.ImageMaker im;\r
\r
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- return;\r
- }\r
-\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
- chooser.getSelectedFile().getParent());\r
-\r
- FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());\r
-\r
- BufferedImage bi = new BufferedImage(width, height,\r
- BufferedImage.TYPE_INT_RGB);\r
- Graphics big = bi.getGraphics();\r
-\r
- big.drawImage(rc.img,0,0,this);\r
-\r
- ImageIO.write(bi, "png", out);\r
- out.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ if(type == jalview.util.ImageMaker.PNG)\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.PNG,\r
+ "Make PNG image from PCA",\r
+ width, height,\r
+ null, null);\r
+ else\r
+ im = new jalview.util.ImageMaker(this,\r
+ jalview.util.ImageMaker.EPS,\r
+ "Make EPS file from PCA",\r
+ width, height,\r
+ null, this.getTitle());\r
+\r
+ if(im.getGraphics()!=null)\r
+ {\r
+ rc.drawBackground(im.getGraphics(), Color.black);\r
+ rc.drawScene(im.getGraphics());\r
+ if (rc.drawAxes == true)\r
+ {\r
+ rc.drawAxes(im.getGraphics());\r
+ }\r
+ im.writeImage();\r
+ }\r
}\r
-\r
}\r
(SequenceI) selsubset.elementAt(j), "pep");\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
- as.printAlignment();\r
+ as.printAlignment(System.out);\r
scores[i][j] = (float) as.getMaxScore() / (float) as.getASeq1().length;\r
totscore = totscore + scores[i][j];\r
\r
\r
import jalview.datamodel.*;\r
\r
-import jalview.io.*;\r
\r
import jalview.schemes.*;\r
\r
JMenuItem sequenceName = new JMenuItem();\r
Sequence sequence;\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
- JMenuItem pdbMenuItem = new JMenuItem();\r
JMenuItem outline = new JMenuItem();\r
JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
JMenu colourMenu = new JMenu();\r
* @param ap DOCUMENT ME!\r
* @param seq DOCUMENT ME!\r
*/\r
- public PopupMenu(AlignmentPanel ap, Sequence seq)\r
+ public PopupMenu(final AlignmentPanel ap, Sequence seq)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
e.printStackTrace();\r
}\r
\r
- if ((seq == null) || (seq.getPDBId() == null))\r
+\r
+ if ((seq != null)\r
+ && seq.getDatasetSequence().getPDBId() != null)\r
{\r
- pdbMenuItem.setVisible(false);\r
+ java.util.Enumeration e = seq.getDatasetSequence().getPDBId().elements();\r
+ while(e.hasMoreElements())\r
+ {\r
+ final PDBEntry pdb = (PDBEntry)e.nextElement();\r
+\r
+ JMenuItem pdbMenuItem = new JMenuItem();\r
+ pdbMenuItem.setText("View PDB entry: "+pdb.getId());\r
+ pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);\r
+ }\r
+ });\r
+ sequenceMenu.add(pdbMenuItem);\r
+ }\r
+\r
}\r
\r
SequenceGroup sg = ap.av.getSelectionGroup();\r
String link = links.elementAt(i).toString();\r
\r
item = new JMenuItem(link.substring(0, link.indexOf("|")));\r
+ String id = sequence.getName();\r
+ if(id.indexOf("|")>-1)\r
+ id = id.substring(id.lastIndexOf("|")+1);\r
\r
final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
- + sequence.getName() +\r
+ + id +\r
link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
\r
\r
unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- pdbMenuItem.setText("View PDB structure");\r
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- pdbMenuItem_actionPerformed(e);\r
- }\r
- });\r
+\r
outline.setText("Border colour");\r
outline.addActionListener(new java.awt.event.ActionListener()\r
{\r
groupMenu.addSeparator();\r
groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
- sequenceMenu.add(pdbMenuItem);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\r
refresh();\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- void pdbMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (sequence.getPDBId() == null)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null,\r
- null);\r
-\r
- PDBfile pdb = new PDBfile(result);\r
-\r
- rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(rc);\r
- Desktop.addInternalFrame(frame,\r
- sequence.getName() + " " + sequence.getPDBId(), 400, 400);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
Desktop.addInternalFrame(frame, "Preferences", 480, 390);\r
frame.setMinimumSize(new Dimension(480,390));\r
\r
- fullID.setSelected( Cache.getDefault("SHOW_FULL_ID", true));\r
+ seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));\r
fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));\r
annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
\r
epsRendering.addItem("Text");\r
epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
\r
+ blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
+ clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
+ fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
+ msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
+ pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
+ pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
+ pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
+\r
/****************************************************\r
* Set up Connections\r
*/\r
public void ok_actionPerformed(ActionEvent e)\r
{\r
\r
- Cache.applicationProperties.setProperty("SHOW_FULL_ID", Boolean.toString(fullID.isSelected()));\r
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
\r
Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
}\r
\r
\r
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
+\r
\r
Cache.saveProperties();\r
try\r
*\r
* @param g DOCUMENT ME!\r
*/\r
- public void paintComponent(Graphics g)\r
+ public void paintComponent(Graphics g1)\r
{\r
\r
+ Graphics2D g = (Graphics2D) g1;\r
+\r
+ g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
+ RenderingHints.VALUE_ANTIALIAS_ON);\r
if(points==null)\r
{\r
g.setFont(new Font("Verdana", Font.PLAIN, 18));\r
*\r
* @param g DOCUMENT ME!\r
*/\r
- public void drawAxes(Graphics g1)\r
+ public void drawAxes(Graphics g)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
-\r
- g.setRenderingHint(RenderingHints.KEY_ANTIALIASING,\r
- RenderingHints.VALUE_ANTIALIAS_ON);\r
\r
g.setColor(Color.yellow);\r
\r
*/\r
public void keyPressed(KeyEvent evt)\r
{\r
- requestFocus();\r
-\r
if (evt.getKeyCode() == KeyEvent.VK_UP)\r
{\r
scalefactor = (float) (scalefactor * 1.1);\r
import java.awt.image.*;\r
\r
import javax.swing.*;\r
+import jalview.schemes.*;\r
\r
\r
/**\r
int LABEL_WEST;\r
int LABEL_EAST;\r
\r
- boolean isOverview = false;\r
-\r
/**\r
* Creates a new SeqCanvas object.\r
*\r
setBackground(Color.white);\r
}\r
\r
+ MCview.PDBCanvas pdbCanvas;\r
+ public SequenceRenderer getSequenceRenderer()\r
+ {\r
+ return sr;\r
+ }\r
+\r
+ public FeatureRenderer getFeatureRenderer()\r
+ {\r
+ return fr;\r
+ }\r
+\r
+ public void setPDBCanvas(MCview.PDBCanvas pc)\r
+ {\r
+ pdbCanvas = pc;\r
+ }\r
+\r
+ public AlignViewport getViewport()\r
+ {\r
+ return av;\r
+ }\r
+\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
// Set this to false to force a full panel paint\r
public void paintComponent(Graphics g)\r
{\r
+ super.paintComponent(g);\r
+\r
sr.renderGaps(av.renderGaps);\r
\r
- if ((img != null) &&\r
- (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
- (getHeight() != g.getClipBounds().height)))\r
+ if ( img != null && (fastPaint\r
+ || (getVisibleRect().width != g.getClipBounds().width)\r
+ || (getVisibleRect().height != g.getClipBounds().height)))\r
{\r
g.drawImage(img, 0, 0, this);\r
fastPaint = false;\r
-\r
return;\r
}\r
\r
+\r
// this draws the whole of the alignment\r
imgWidth = getWidth();\r
imgHeight = getHeight();\r
return;\r
}\r
\r
-\r
img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
gg = (Graphics2D) img.getGraphics();\r
gg.setFont(av.getFont());\r
}\r
\r
g.drawImage(img, 0, 0, this);\r
+\r
+ if (pdbCanvas != null)\r
+ {\r
+ pdbCanvas.updateSeqColours();\r
+ }\r
+\r
}\r
\r
/**\r
repaint();\r
}\r
\r
+\r
synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
int y2, int startx, int starty, int offset)\r
{\r
- Graphics2D g = (Graphics2D) g1;\r
- g.setFont(av.getFont());\r
+ Graphics2D g = (Graphics2D) g1;\r
+ g.setFont(av.getFont());\r
\r
+ SequenceI nextSeq, dna = null;\r
+ int aaHeight = av.charHeight, dnaHeight = av.charHeight;\r
+ Font dnafont = null, aafont = av.getFont();\r
\r
- SequenceI nextSeq;\r
+ /* if (av.getShowTranslation())\r
+ {\r
+ aaHeight = (int) (av.getCharHeight() * aaRatio);\r
+ dnaHeight = (int) (av.getCharHeight() * (1 - aaRatio));\r
+ java.awt.geom.AffineTransform transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1f / 3f, 1);\r
+ dnafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ dnaHeight);\r
+ dnafont = dnafont.deriveFont(transform);\r
+\r
+ aafont = new Font(av.getFont().getName(), av.getFont().getStyle(),\r
+ aaHeight);\r
+ transform = new java.awt.geom.AffineTransform();\r
+ transform.scale(1 / aaRatio, 1);\r
+ aafont = aafont.deriveFont(transform);\r
+ }\r
+*/\r
\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
\r
/// First draw the sequences\r
/////////////////////////////\r
for (int i = y1; i < y2; i++)\r
{\r
nextSeq = av.alignment.getSequenceAt(i);\r
- g.setFont(av.getFont());\r
-\r
+ g.setFont(aafont);\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ dna = nextSeq;\r
+ StringBuffer sb = new StringBuffer();\r
+ for(int r = 0; r<nextSeq.getLength(); r+=3)\r
+ {\r
+ String codon = nextSeq.getSequence(r, r+3);\r
+ codon = codon.replace('U', 'T');\r
+ String res = ResidueProperties.codonTranslate(codon);\r
+ if(res !=null )\r
+ {\r
+ if (res.equals("STOP"))\r
+ sb.append("X");\r
+ else\r
+ sb.append(res);\r
+ }\r
+ }\r
+ nextSeq = new Sequence("d", sb.toString());\r
+ }*/\r
\r
sr.drawSequence(g, nextSeq, av.alignment.findAllGroups(nextSeq),\r
x1, x2, (x1 - startx) * av.charWidth,\r
offset + ( (i - starty) * av.charHeight), av.charWidth,\r
- av.charHeight);\r
-\r
-\r
+ aaHeight);\r
\r
+ /* if(av.getShowTranslation())\r
+ {\r
+ av.setGlobalColourScheme(new NucleotideColourScheme());\r
+ g.setFont(dnafont);\r
+ sr.drawSequence(g, dna, null,\r
+ x1*3, (x2+2) * 3, ( (x1 - startx) * av.charWidth) / 3,\r
+ offset + ( (i - starty) * av.charHeight) + aaHeight,\r
+ av.charWidth / 3,\r
+ dnaHeight);\r
+ av.setGlobalColourScheme(cs);\r
+ }*/\r
\r
if (av.showSequenceFeatures)\r
{\r
- fr.drawSequence(g, nextSeq,\r
- av.alignment.findAllGroups(nextSeq), x1, x2,\r
+ fr.drawSequence(g, nextSeq, x1, x2,\r
(x1 - startx) * av.charWidth,\r
offset + ((i - starty) * av.charHeight), av.charWidth,\r
av.charHeight);\r
// Now outline any areas if necessary\r
/////////////////////////////////////\r
SequenceGroup group = av.getSelectionGroup();\r
- java.util.Vector groups = av.alignment.getGroups();\r
\r
int sx = -1;\r
int sy = -1;\r
int ex = -1;\r
int groupIndex = -1;\r
\r
- if ((group == null) && (groups.size() > 0))\r
+ if ((group == null) && (av.alignment.getGroups().size() > 0))\r
{\r
- group = (SequenceGroup) groups.elementAt(0);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(0);\r
groupIndex = 0;\r
}\r
\r
-\r
- if (group != null && !isOverview)\r
+ if (group != null)\r
{\r
do\r
{\r
\r
groupIndex++;\r
\r
- if (groupIndex >= groups.size())\r
+ if (groupIndex >= av.alignment.getGroups().size())\r
{\r
break;\r
}\r
\r
- group = (SequenceGroup) groups.elementAt(groupIndex);\r
+ group = (SequenceGroup) av.alignment.getGroups().elementAt(groupIndex);\r
}\r
- while (groupIndex < groups.size());\r
+ while (groupIndex < av.alignment.getGroups().size());\r
}\r
\r
/// Highlight search Results once all sequences have been drawn\r
\r
ap = p;\r
\r
+\r
addMouseMotionListener(new MouseMotionAdapter()\r
{\r
public void mouseMoved(MouseEvent evt)\r
{\r
doMouseMoved(evt);\r
+ if (editingSeqs)\r
+ {\r
+ // This is because MacOSX creates a mouseMoved\r
+ // If control is down\r
+ if(!av.isDataset())\r
+ doMouseDragged(evt);\r
+ }\r
}\r
\r
public void mouseDragged(MouseEvent evt)\r
{\r
if (editingSeqs)\r
{\r
+ if(!av.isDataset())\r
doMouseDragged(evt);\r
}\r
else\r
{\r
+ if(!av.isDataset())\r
doMouseDraggedDefineMode(evt);\r
}\r
}\r
{\r
Font font = av.getFont();\r
int fontSize = font.getSize();\r
- if (e.getWheelRotation() > 0 && fontSize < 30)\r
+ if (e.getWheelRotation() > 0 && fontSize < 51)\r
fontSize++;\r
else if (fontSize > 1)\r
fontSize--;\r
});\r
\r
\r
- addMouseListener(new MouseAdapter()\r
- {\r
- public void mouseReleased(MouseEvent evt)\r
- {\r
- mouseWheelPressed = false;\r
-\r
- if (editingSeqs)\r
- {\r
- doMouseReleased(evt);\r
- }\r
- else\r
- {\r
- doMouseReleasedDefineMode(evt);\r
- }\r
- }\r
-\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if( javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
- {\r
- mouseWheelPressed = true;\r
- return;\r
- }\r
+ if(!av.isDataset())\r
+ {\r
+ addMouseListener(new MouseAdapter()\r
+ {\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ mouseWheelPressed = false;\r
\r
- if (evt.isShiftDown() || evt.isAltDown() ||\r
- evt.isControlDown())\r
- {\r
- if (evt.isAltDown() || evt.isControlDown())\r
- {\r
- groupEditing = true;\r
- }\r
+ if (editingSeqs)\r
+ {\r
+ doMouseReleased(evt);\r
+ }\r
+ else\r
+ {\r
+ doMouseReleasedDefineMode(evt);\r
+ }\r
+ }\r
\r
- editingSeqs = true;\r
- doMousePressed(evt);\r
- }\r
- else\r
- {\r
- doMousePressedDefineMode(evt);\r
- }\r
- }\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ if (javax.swing.SwingUtilities.isMiddleMouseButton(evt))\r
+ {\r
+ mouseWheelPressed = true;\r
+ return;\r
+ }\r
+\r
+ if (evt.isShiftDown() || evt.isAltDown() ||\r
+ evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown() || evt.isControlDown())\r
+ {\r
+ groupEditing = true;\r
+\r
+ }\r
+\r
+ editingSeqs = true;\r
+ doMousePressed(evt);\r
+ }\r
+ else\r
+ {\r
+ doMousePressedDefineMode(evt);\r
+ }\r
+ }\r
\r
- public void mouseExited(MouseEvent evt)\r
- {\r
- if (editingSeqs)\r
- {\r
- return;\r
- }\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
\r
- doMouseExitedDefineMode(evt);\r
- }\r
+ doMouseExitedDefineMode(evt);\r
+ }\r
\r
- public void mouseEntered(MouseEvent evt)\r
- {\r
- if (editingSeqs)\r
- {\r
- return;\r
- }\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ if (editingSeqs)\r
+ {\r
+ return;\r
+ }\r
\r
- doMouseEnteredDefineMode(evt);\r
- }\r
- });\r
+ doMouseEnteredDefineMode(evt);\r
+ }\r
+ });\r
+ }\r
}\r
\r
int startWrapBlock=-1;\r
return;\r
}\r
\r
+ if(seqCanvas.pdbCanvas!=null && sequence==seqCanvas.pdbCanvas.sequence)\r
+ {\r
+ seqCanvas.pdbCanvas.highlightRes(sequence.findPosition(res));\r
+ }\r
+\r
+\r
StringBuffer text = new StringBuffer("Sequence " + (seq + 1) + " ID: " +\r
sequence.getName());\r
\r
// use aa to see if the mouse pointer is on a\r
if (av.showSequenceFeatures)\r
{\r
- Vector features = sequence.getSequenceFeatures();\r
- Enumeration e = features.elements();\r
- StringBuffer sbuffer = new StringBuffer();\r
-\r
- while (e.hasMoreElements())\r
+ Vector features = sequence.getDatasetSequence().getSequenceFeatures();\r
+ if(features!=null)\r
{\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ StringBuffer sbuffer = new StringBuffer("<html>");\r
\r
- if ((sf.getStart() <= sequence.findPosition(res)) &&\r
- (sf.getEnd() >= sequence.findPosition(res)))\r
+ for (int i = 0; i < features.size(); i++)\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) features.elementAt(i);\r
+\r
+ if ( (sf.getBegin() <= sequence.findPosition(res)) &&\r
+ (sf.getEnd() >= sequence.findPosition(res)))\r
{\r
- if (sbuffer.length() > 0)\r
+ if (sf.getType().equals("disulfide bond"))\r
+ {\r
+ if (sf.getBegin() == sequence.findPosition(res)\r
+ || sf.getEnd() == sequence.findPosition(res))\r
{\r
- sbuffer.append("; ");\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ sbuffer.append("disulfide bond " + sf.getBegin() + ":" +\r
+ sf.getEnd());\r
}\r
+ }\r
+ else\r
+ {\r
+ if (sbuffer.length() > 6)\r
+ sbuffer.append("<br>");\r
+ sbuffer.append(sf.getType());\r
+ if (sf.getDescription() != null)\r
+ sbuffer.append(" " + sf.getDescription());\r
\r
- sbuffer.append(sf.getType() + " " + sf.getDescription());\r
-\r
- if (sf.getStatus().length() > 0)\r
+ if (sf.getStatus() != null)\r
{\r
- sbuffer.append(" (" + sf.getStatus() + ")");\r
+ sbuffer.append(" (" + sf.getStatus() + ")");\r
}\r
+ }\r
}\r
- }\r
\r
- this.setToolTipText(sbuffer.toString());\r
+ }\r
+\r
+ sbuffer.append("</html>");\r
+ if(sbuffer.length()==13) // <html></html>\r
+ setToolTipText("");\r
+ else\r
+ setToolTipText(sbuffer.toString());\r
+ }\r
+ else\r
+ setToolTipText("");\r
}\r
}\r
\r
\r
try\r
{\r
- Thread.sleep(75);\r
+ Thread.sleep(20);\r
}\r
catch (Exception ex)\r
{\r
--- /dev/null
+package jalview.gui;\r
+\r
+import javax.swing.*;\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import jalview.io.EBIFetchClient;\r
+import MCview.*;\r
+import jalview.datamodel.*;\r
+import jalview.analysis.AlignSeq;\r
+import java.io.File;\r
+import jalview.io.*;\r
+import java.util.*;\r
+\r
+\r
+public class SequenceFetcher\r
+ extends JPanel implements Runnable\r
+{\r
+ JInternalFrame frame;\r
+ AlignFrame alignFrame;\r
+ StringBuffer result;\r
+ public SequenceFetcher(AlignFrame af)\r
+ {\r
+ alignFrame = af;\r
+ database.addItem("-- Select Database --");\r
+ database.addItem("Uniprot");\r
+ database.addItem("EMBL");\r
+ database.addItem("EMBLCDS");\r
+ database.addItem("PDB");\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ frame = new JInternalFrame();\r
+ frame.setContentPane(this);\r
+ if(System.getProperty("os.name").startsWith("Mac"))\r
+ Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
+ else\r
+ Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 120);\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.setLayout(gridBagLayout1);\r
+\r
+ database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ database.setMinimumSize(new Dimension(160, 21));\r
+ database.setPreferredSize(new Dimension(160, 21));\r
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ jLabel1.setText(\r
+ "Separate multiple accession ids with semi colon \";\"");\r
+ ok.setText("OK");\r
+ ok.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ cancel.setText("Cancel");\r
+ cancel.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ cancel_actionPerformed(e);\r
+ }\r
+ });\r
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ textfield.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ok_actionPerformed(e);\r
+ }\r
+ });\r
+ jPanel1.add(ok);\r
+ jPanel1.add(cancel);\r
+ this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
+ , GridBagConstraints.WEST,\r
+ GridBagConstraints.NONE,\r
+ new Insets(7, 4, 0, 6), 77, 6));\r
+ this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
+ , GridBagConstraints.WEST,\r
+ GridBagConstraints.BOTH,\r
+ new Insets(7, -2, 7, 12), 241, -2));\r
+ this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
+ , GridBagConstraints.WEST,\r
+ GridBagConstraints.NONE,\r
+ new Insets(0, 4, 0, 0), 1, 0));\r
+ this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
+ , GridBagConstraints.CENTER,\r
+ GridBagConstraints.HORIZONTAL,\r
+ new Insets(0, 0, 0, 6), 200, 1));\r
+ }\r
+\r
+ JComboBox database = new JComboBox();\r
+ JLabel jLabel1 = new JLabel();\r
+ JButton ok = new JButton();\r
+ JButton cancel = new JButton();\r
+ JPanel jPanel1 = new JPanel();\r
+ JTextField textfield = new JTextField();\r
+ GridBagLayout gridBagLayout1 = new GridBagLayout();\r
+ public void cancel_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setClosed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+\r
+ public void ok_actionPerformed(ActionEvent e)\r
+ {\r
+ frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
+ database.setEnabled(false);\r
+ textfield.setEnabled(false);\r
+ ok.setEnabled(false);\r
+ cancel.setEnabled(false);\r
+\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ result = new StringBuffer();\r
+ if (database.getSelectedItem().equals("Uniprot"))\r
+ {\r
+ getUniprotFile(textfield.getText());\r
+ }\r
+ else if (database.getSelectedItem().equals("EMBL")\r
+ || database.getSelectedItem().equals("EMBLCDS"))\r
+ {\r
+ EBIFetchClient dbFetch = new EBIFetchClient();\r
+ String[] reply = dbFetch.fetchData(\r
+ database.getSelectedItem().toString().toLowerCase(\r
+ ) + ":" + textfield.getText(),\r
+ "fasta", "raw");\r
+\r
+ for (int i = 0; i < reply.length; i++)\r
+ result.append(reply[i] + "\n");\r
+\r
+ parseResult(result.toString());\r
+ }\r
+ else if (database.getSelectedItem().equals("PDB"))\r
+ {\r
+ result = getPDBFile(textfield.getText().toUpperCase());\r
+ parseResult(result.toString());\r
+ }\r
+\r
+\r
+ if (result == null || result.length() == 0)\r
+ showErrorMessage("Error retrieving " + textfield.getText()\r
+ + " from " + database.getSelectedItem());\r
+\r
+\r
+ database.setEnabled(true);\r
+ textfield.setEnabled(true);\r
+ ok.setEnabled(true);\r
+ cancel.setEnabled(true);\r
+ frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
+ }\r
+\r
+ void getUniprotFile(String id)\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
+ SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
+ Vector entries = sff.getUniprotEntries(file);\r
+\r
+ if(entries!=null)\r
+ {\r
+ //First, make the new sequences\r
+ Enumeration en = entries.elements();\r
+ while (en.hasMoreElements())\r
+ {\r
+ UniprotEntry entry = (UniprotEntry) en.nextElement();\r
+ StringBuffer name = new StringBuffer( ">Uniprot/Swiss-Prot" );\r
+ Enumeration en2 = entry.getAccession().elements();\r
+ while(en2.hasMoreElements())\r
+ {\r
+ name.append("|");\r
+ name.append(en2.nextElement());\r
+ }\r
+ en2 = entry.getName().elements();\r
+ while(en2.hasMoreElements())\r
+ {\r
+ name.append("|");\r
+ name.append(en2.nextElement());\r
+ }\r
+\r
+ if(entry.getProteinName()!=null)\r
+ name.append(" "+entry.getProteinName().elementAt(0));\r
+\r
+ result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
+\r
+ }\r
+\r
+ //Then read in the features and apply them to the dataset\r
+ SequenceI [] sequence = parseResult(result.toString());\r
+ for(int i=0; i<entries.size(); i++)\r
+ {\r
+ UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
+ Enumeration e = entry.getDbReference().elements();\r
+ Vector onlyPdbEntries = new Vector();\r
+ while (e.hasMoreElements())\r
+ {\r
+ PDBEntry pdb = (PDBEntry) e.nextElement();\r
+ if (!pdb.getType().equals("PDB"))\r
+ continue;\r
+\r
+ onlyPdbEntries.addElement(pdb);\r
+ }\r
+\r
+ sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
+ sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
+\r
+ }\r
+ }\r
+ }\r
+\r
+ StringBuffer getPDBFile(String id)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ String chain = null;\r
+ if (id.indexOf(":") > -1)\r
+ {\r
+ chain = id.substring(id.indexOf(":") + 1);\r
+ id = id.substring(0, id.indexOf(":"));\r
+ }\r
+\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
+ try\r
+ {\r
+ PDBfile pdbfile = new PDBfile(reply);\r
+ for (int i = 0; i < pdbfile.chains.size(); i++)\r
+ {\r
+ if (chain == null ||\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
+ toUpperCase().equals(chain))\r
+ result.append("\n>PDB|" + id + "|" +\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
+ getName() +\r
+ "\n"\r
+ +\r
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
+ getSequence());\r
+ }\r
+ }\r
+ catch (Exception ex) // Problem parsing PDB file\r
+ {\r
+ showErrorMessage("Error retrieving " + textfield.getText() + " from " +\r
+ database.getSelectedItem());\r
+ return null;\r
+ }\r
+\r
+ return result;\r
+ }\r
+\r
+ SequenceI[] parseResult(String result)\r
+ {\r
+ String format = IdentifyFile.Identify(result, "Paste");\r
+ SequenceI[] sequences = null;\r
+\r
+ if (FormatAdapter.formats.contains(format))\r
+ {\r
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
+ if (sequences != null && sequences.length>0)\r
+ {\r
+ if(alignFrame==null)\r
+ {\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ af.currentFileFormat = format;\r
+ Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
+ AlignFrame.NEW_WINDOW_WIDTH,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.statusBar.setText("Successfully pasted alignment file");\r
+ try\r
+ {\r
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ alignFrame.viewport.alignment.addSequence(sequences[i]);\r
+\r
+ ////////////////////////////\r
+ //Datset needs extension;\r
+ /////////////////////////////\r
+ Sequence ds = new Sequence(sequences[i].getName(),\r
+ AlignSeq.extractGaps("-. ",\r
+ sequences[i].getSequence()),\r
+ sequences[i].getStart(),\r
+ sequences[i].getEnd());\r
+ sequences[i].setDatasetSequence(ds);\r
+ alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
+ }\r
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
+ getHeight());\r
+ alignFrame.viewport.alignment.getWidth();\r
+ alignFrame.viewport.firePropertyChange("alignment", null,\r
+ alignFrame.viewport.getAlignment().getSequences());\r
+\r
+ }\r
+\r
+ if (database.getSelectedItem().equals("PDB"))\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\r
+ {\r
+ PDBEntry entry = new PDBEntry();\r
+ entry.setId(textfield.getText());\r
+ sequences[i].getDatasetSequence().addPDBId(entry);\r
+ }\r
+ }\r
+\r
+ }\r
+ else\r
+ showErrorMessage( "Error retrieving "+textfield.getText()\r
+ +" from "+database.getSelectedItem());\r
+ }\r
+\r
+ return sequences;\r
+\r
+ }\r
+\r
+ void showErrorMessage(String error)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
+ }\r
+}\r
+\r
+\r
+\r
+\r
\r
import java.awt.*;\r
\r
-\r
/**\r
* DOCUMENT ME!\r
*\r
renderGaps = b;\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param cs DOCUMENT ME!\r
- * @param seq DOCUMENT ME!\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+\r
+ public Color getResidueBoxColour(SequenceI seq, int i)\r
{\r
- getBoxColour(cs, seq, i);\r
+ allGroups = av.alignment.findAllGroups(seq);\r
\r
- return resBoxColour;\r
+ if (inCurrentSequenceGroup(i))\r
+ {\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
+ {\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
+ }\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
+ }\r
+\r
+ return resBoxColour;\r
}\r
\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
\r
graphics = g;\r
\r
- drawBoxes(seq, start, end, x1, y1, width, height);\r
+ drawBoxes(seq, start, end, x1, y1, (int) width, height);\r
\r
fm = g.getFontMetrics();\r
- drawText(seq, start, end, x1, y1, width, height);\r
+ drawText(seq, start, end, x1, y1, (int) width, height);\r
}\r
\r
/**\r
* @param width DOCUMENT ME!\r
* @param height DOCUMENT ME!\r
*/\r
- public void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
+ public synchronized void drawBoxes(SequenceI seq, int start, int end, int x1, int y1,\r
int width, int height)\r
{\r
- int i = start;\r
- int length = seq.getLength();\r
+ int i = start;\r
+ int length = seq.getLength();\r
\r
- int curStart = -1;\r
- int curWidth = width;\r
+ int curStart = -1;\r
+ int curWidth = width;\r
\r
- Color tempColour = null;\r
+ Color tempColour = null;\r
\r
- while (i <= end)\r
- {\r
- resBoxColour = Color.white;\r
+ while (i <= end)\r
+ {\r
+ resBoxColour = Color.white;\r
\r
- if (i < length)\r
+ if (i < length)\r
+ {\r
+ if (inCurrentSequenceGroup(i))\r
{\r
- if (inCurrentSequenceGroup(i))\r
- {\r
- if (currentSequenceGroup.getDisplayBoxes())\r
- {\r
- getBoxColour(currentSequenceGroup.cs, seq, i);\r
- }\r
- }\r
- else if (av.getShowBoxes())\r
+ if (currentSequenceGroup.getDisplayBoxes())\r
{\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+ getBoxColour(currentSequenceGroup.cs, seq, i);\r
}\r
-\r
+ }\r
+ else if (av.getShowBoxes())\r
+ {\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
}\r
\r
- if (resBoxColour != tempColour)\r
- {\r
- if (tempColour != null)\r
- {\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
- curWidth, height);\r
- }\r
+ }\r
\r
- graphics.setColor(resBoxColour);\r
+ if (resBoxColour != tempColour)\r
+ {\r
+ if (tempColour != null)\r
+ {\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1,\r
+ curWidth, height);\r
+ }\r
\r
- curStart = i;\r
- curWidth = width;\r
- tempColour = resBoxColour;\r
- }\r
- else\r
- {\r
- curWidth += width;\r
- }\r
+ graphics.setColor(resBoxColour);\r
\r
- i++;\r
- }\r
+ curStart = i;\r
+ curWidth = width;\r
+ tempColour = resBoxColour;\r
+ }\r
+ else\r
+ {\r
+ curWidth += width;\r
+ }\r
+\r
+ i++;\r
+ }\r
+\r
+ graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
+ height);\r
\r
- graphics.fillRect(x1 + (width * (curStart - start)), y1, curWidth,\r
- height);\r
}\r
\r
/**\r
int charOffset = 0;\r
char s;\r
\r
+\r
// Need to find the sequence position here.\r
String sequence = seq.getSequence();\r
\r
\r
if (av.getColourText())\r
{\r
- getBoxColour(av.getGlobalColourScheme(), seq, i);\r
+ getBoxColour(av.globalColourScheme, seq, i);\r
\r
if (av.getShowBoxes())\r
{\r
charOffset = (width - fm.charWidth(s)) / 2;\r
graphics.drawString(String.valueOf(s),\r
charOffset + x1 + (int)(width * (i - start)), (y1 + height) - pady);\r
+\r
}\r
}\r
\r
\r
int y = yoffset;\r
\r
- g.drawString("Jalview 2005 ", 50, y);\r
+ g.drawString("Jalview "+jalview.bin.Cache.getProperty("VERSION"), 50, y);\r
+\r
+ FontMetrics fm = g.getFontMetrics();\r
+ int vwidth = fm.stringWidth("Jalview "+jalview.bin.Cache.getProperty("VERSION"));\r
g.setFont(new Font("Verdana", Font.BOLD, fontSize + 2));\r
- g.drawString("Version " + jalview.bin.Cache.getProperty("VERSION") +\r
- "; Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),\r
- 180, y);\r
+ g.drawString("Last updated: " + jalview.bin.Cache.getDefault("BUILD_DATE", "unknown"),\r
+ 50 + vwidth +5, y);\r
\r
if (jalview.bin.Cache.getDefault("LATEST_VERSION", "Checking").equals("Checking"))\r
{\r
git://source.jalview.org / jalview.git / commitdiff