import jalview.datamodel.ColumnSelection;\r
import jalview.datamodel.PDBEntry;\r
import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceCollectionI;\r
import jalview.datamodel.SequenceGroup;\r
import jalview.datamodel.SequenceI;\r
import jalview.io.AnnotationFile;\r
import java.net.URLEncoder;\r
import java.util.Enumeration;\r
import java.util.Hashtable;\r
+import java.util.List;\r
import java.util.StringTokenizer;\r
import java.util.Vector;\r
\r
* @param type is protocol for accessing data referred to by file\r
*/\r
\r
- public void parseFeaturesFile(String file, String type)\r
+ public boolean parseFeaturesFile(String file, String type)\r
{\r
- parseFeaturesFile(file, type, true);\r
+ return parseFeaturesFile(file, type, true);\r
}\r
\r
/**\r
* @param file file URL, content, or other resolvable path\r
* @param type is protocol for accessing data referred to by file\r
* @param autoenabledisplay when true, display features flag will be automatically enabled if features are loaded\r
+ * @return true if data parsed as a features file\r
*/\r
- public void parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
+ public boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
{ \r
+ // TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.\r
+ \r
Hashtable featureLinks = new Hashtable();\r
boolean featuresFile = false;\r
try\r
viewport.featureSettings.refreshTable();\r
}\r
alignPanel.paintAlignment(true);\r
+ statusBar.setText("Successfully added features to alignment.");\r
}\r
-\r
+ return featuresFile;\r
}\r
\r
public void keyPressed(KeyEvent evt)\r
{\r
loadAnnotations();\r
}\r
- else if( source == loadScores ) {\r
- loadScores();\r
- }\r
else if (source == outputAnnotations)\r
{\r
outputAnnotations(true);\r
else if (source == clustalColour)\r
{\r
abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(\r
- viewport.getAlignment().getSequences(),\r
- viewport.getAlignment().getWidth()));\r
+ changeColour(new ClustalxColourScheme(viewport.getAlignment(),null));\r
}\r
else if (source == zappoColour)\r
{\r
public void loadAnnotations()\r
{\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
- cap.setText("Paste your features / annotations file here.");\r
+ cap.setText("Paste your features / annotations / T-coffee score file here.");\r
cap.setAnnotationImport();\r
Frame frame = new Frame();\r
frame.add(cap);\r
\r
}\r
\r
- public void loadScores() {\r
- //TODO\r
- \r
- }\r
-\r
public String outputAnnotations(boolean displayTextbox)\r
{\r
String annotation = new AnnotationFile().printAnnotations(\r
public void closeMenuItem_actionPerformed()\r
{\r
PaintRefresher.RemoveComponent(alignPanel);\r
- PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
- PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+ if (alignPanel.seqPanel!=null && alignPanel.seqPanel.seqCanvas!=null)\r
+ {\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ }\r
+ if (alignPanel.idPanel!=null && alignPanel.idPanel.idCanvas!=null) {\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+ }\r
\r
if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
{\r
\r
synchronized void slideSequences(boolean right, int size)\r
{\r
- Vector sg = new Vector();\r
+ List<SequenceI>sg = new Vector<SequenceI>();\r
if (viewport.cursorMode)\r
{\r
- sg.addElement(viewport.getAlignment()\r
+ sg.add(viewport.getAlignment()\r
.getSequenceAt(alignPanel.seqPanel.seqCanvas.cursorY));\r
}\r
else if (viewport.getSelectionGroup() != null\r
return;\r
}\r
\r
- Vector invertGroup = new Vector();\r
+ Vector<SequenceI> invertGroup = new Vector();\r
\r
for (int i = 0; i < viewport.getAlignment().getHeight(); i++)\r
{\r
invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));\r
}\r
\r
- SequenceI[] seqs1 = new SequenceI[sg.size()];\r
- for (int i = 0; i < sg.size(); i++)\r
- seqs1[i] = (SequenceI) sg.elementAt(i);\r
+ SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);\r
\r
- SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+ SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup.size()]);\r
for (int i = 0; i < invertGroup.size(); i++)\r
seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
\r
Color col = new Color((int) (Math.random() * 255),\r
(int) (Math.random() * 255), (int) (Math.random() * 255));\r
col = col.brighter();\r
- for (Enumeration sq = gps[g].getSequences(null).elements(); sq\r
- .hasMoreElements(); viewport.setSequenceColour(\r
- (SequenceI) sq.nextElement(), col))\r
+ for (SequenceI sq : gps[g].getSequences(null))\r
+ viewport.setSequenceColour(\r
+ sq, col)\r
;\r
}\r
PaintRefresher.Refresh(this, viewport.getSequenceSetId());\r
\r
addHistoryItem(trimRegion);\r
\r
- Vector groups = viewport.getAlignment().getGroups();\r
\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
+ for (SequenceGroup sg:viewport.getAlignment().getGroups())\r
+ {\r
if ((trimLeft && !sg.adjustForRemoveLeft(column))\r
|| (!trimLeft && !sg.adjustForRemoveRight(column)))\r
{\r
overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
+ final AlignmentPanel ap=alignPanel;\r
frame.addWindowListener(new WindowAdapter()\r
{\r
public void windowClosing(WindowEvent e)\r
{\r
- alignPanel.setOverviewPanel(null);\r
+ if (ap!=null) {\r
+ ap.setOverviewPanel(null);\r
+ }\r
};\r
});\r
\r
} \r
viewport.setGlobalColourScheme(cs);\r
\r
- if (viewport.getColourAppliesToAllGroups())\r
- {\r
- Vector groups = viewport.getAlignment().getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (cs == null)\r
- {\r
- sg.cs = null;\r
- continue;\r
- }\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- sg.cs = new ClustalxColourScheme(\r
- sg.getSequences(viewport.getHiddenRepSequences()),\r
- sg.getWidth());\r
- }\r
- else\r
- {\r
- try\r
- {\r
- sg.cs = cs.getClass().newInstance();\r
- } catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- sg.cs = cs;\r
- }\r
- }\r
-\r
- if (viewport.getAbovePIDThreshold()\r
- || cs instanceof PIDColourScheme\r
- || cs instanceof Blosum62ColourScheme)\r
- {\r
- sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(\r
- sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
- sg.getWidth()));\r
- }\r
- else\r
- {\r
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- if (viewport.getConservationSelected())\r
- {\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3,\r
- sg.getSequences(viewport.getHiddenRepSequences()), 0,\r
- viewport.getAlignment().getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.getConsPercGaps());\r
- sg.cs.setConservation(c);\r
- }\r
- else\r
- {\r
- sg.cs.setConservation(null);\r
- sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
- }\r
-\r
- }\r
- }\r
\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
\r
MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
\r
- MenuItem loadScores = new MenuItem("Load Associated T-Coffee scores ...");\r
-\r
MenuItem outputFeatures = new MenuItem("Export Features ...");\r
\r
MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
\r
loadTree.addActionListener(this);\r
loadAnnotations.addActionListener(this);\r
- loadScores.addActionListener(this);\r
outputFeatures.addActionListener(this);\r
outputAnnotations.addActionListener(this);\r
selectAllSequenceMenuItem.addActionListener(this);\r
fileMenu.add(inputText);\r
fileMenu.add(loadTree);\r
fileMenu.add(loadAnnotations);\r
- fileMenu.add(loadScores);\r
\r
fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
git://source.jalview.org / jalview.git / blobdiff