*/\r
package jalview.appletgui;\r
\r
-import java.net.*;\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.analysis.*;\r
+import jalview.analysis.AAFrequency;\r
+import jalview.analysis.AlignmentSorter;\r
+import jalview.analysis.Conservation;\r
import jalview.api.SequenceStructureBinding;\r
import jalview.bin.JalviewLite;\r
-import jalview.commands.*;\r
-import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.OrderCommand;\r
+import jalview.commands.RemoveGapColCommand;\r
+import jalview.commands.RemoveGapsCommand;\r
+import jalview.commands.SlideSequencesCommand;\r
+import jalview.commands.TrimRegionCommand;\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.AlignmentOrder;\r
+import jalview.datamodel.ColumnSelection;\r
+import jalview.datamodel.PDBEntry;\r
+import jalview.datamodel.Sequence;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.io.AnnotationFile;\r
+import jalview.io.AppletFormatAdapter;\r
+import jalview.io.FeaturesFile;\r
+import jalview.io.TCoffeeScoreFile;\r
+import jalview.schemes.Blosum62ColourScheme;\r
+import jalview.schemes.BuriedColourScheme;\r
+import jalview.schemes.ClustalxColourScheme;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.schemes.HelixColourScheme;\r
+import jalview.schemes.HydrophobicColourScheme;\r
+import jalview.schemes.NucleotideColourScheme;\r
+import jalview.schemes.PIDColourScheme;\r
+import jalview.schemes.PurinePyrimidineColourScheme;\r
+import jalview.schemes.RNAHelicesColourChooser;\r
+import jalview.schemes.ResidueProperties;\r
+import jalview.schemes.StrandColourScheme;\r
+import jalview.schemes.TCoffeeColourScheme;\r
+import jalview.schemes.TaylorColourScheme;\r
+import jalview.schemes.TurnColourScheme;\r
+import jalview.schemes.ZappoColourScheme;\r
import jalview.structure.StructureSelectionManager;\r
\r
-public class AlignFrame extends EmbmenuFrame implements ActionListener,\r
- ItemListener, KeyListener\r
+import java.awt.BorderLayout;\r
+import java.awt.Canvas;\r
+import java.awt.CheckboxMenuItem;\r
+import java.awt.Color;\r
+import java.awt.Font;\r
+import java.awt.FontMetrics;\r
+import java.awt.Frame;\r
+import java.awt.Graphics;\r
+import java.awt.Label;\r
+import java.awt.Menu;\r
+import java.awt.MenuBar;\r
+import java.awt.MenuItem;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.FocusEvent;\r
+import java.awt.event.FocusListener;\r
+import java.awt.event.ItemEvent;\r
+import java.awt.event.ItemListener;\r
+import java.awt.event.KeyEvent;\r
+import java.awt.event.KeyListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.io.IOException;\r
+import java.io.InputStreamReader;\r
+import java.net.URL;\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
+public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
{\r
public AlignmentPanel alignPanel;\r
\r
int DEFAULT_HEIGHT = 500;\r
\r
String jalviewServletURL;\r
+ \r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,\r
- String title, boolean embedded)\r
+ public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
{\r
-\r
if (applet != null)\r
{\r
jalviewServletURL = applet.getParameter("APPLICATION_URL");\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
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
{\r
changeColour(new Blosum62ColourScheme());\r
}\r
+ else if (source == tcoffeeColour) {\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ }\r
else if (source == annotationColour)\r
{\r
new AnnotationColourChooser(viewport, alignPanel);\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
jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
\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
\r
/**\r
- * DOCUMENT ME!\r
+ * TODO: JAL-1104\r
*/\r
void updateEditMenuBar()\r
{\r
}\r
}\r
\r
+ /**\r
+ * TODO: JAL-1104\r
+ */\r
public void addHistoryItem(CommandI command)\r
{\r
if (command.getSize() > 0)\r
}\r
\r
/**\r
+ * TODO: JAL-1104\r
* DOCUMENT ME!\r
* \r
* @param e\r
}\r
\r
/**\r
+ * TODO: JAL-1104\r
* DOCUMENT ME!\r
* \r
* @param e\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
cs.setConsensus(viewport.getSequenceConsensusHash());\r
\r
- }\r
+ } \r
viewport.setGlobalColourScheme(cs);\r
\r
if (viewport.getColourAppliesToAllGroups())\r
{\r
try\r
{\r
- sg.cs = (ColourSchemeI) cs.getClass().newInstance();\r
+ sg.cs = cs.getClass().newInstance();\r
} catch (Exception ex)\r
{\r
ex.printStackTrace();\r
MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
\r
MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
-\r
+ \r
MenuItem outputFeatures = new MenuItem("Export Features ...");\r
\r
MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
MenuItem PIDColour = new MenuItem();\r
\r
MenuItem BLOSUM62Colour = new MenuItem();\r
+ \r
+ MenuItem tcoffeeColour = new MenuItem();\r
\r
MenuItem njTreeBlosumMenuItem = new MenuItem();\r
\r
PIDColour.addActionListener(this);\r
BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
BLOSUM62Colour.addActionListener(this);\r
- avDistanceTreeBlosumMenuItem\r
- .setLabel("Average Distance Using BLOSUM62");\r
+ tcoffeeColour.setLabel("T-Coffee Scores");\r
+ tcoffeeColour.setEnabled(false); // it will enabled only if a score file is provided\r
+ tcoffeeColour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem .setLabel("Average Distance Using BLOSUM62");\r
avDistanceTreeBlosumMenuItem.addActionListener(this);\r
njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
njTreeBlosumMenuItem.addActionListener(this);\r
fileMenu.add(inputText);\r
fileMenu.add(loadTree);\r
fileMenu.add(loadAnnotations);\r
-\r
+ \r
fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
fileMenu.add(outputFeatures);\r
colourMenu.add(buriedColour);\r
colourMenu.add(nucleotideColour);\r
colourMenu.add(purinePyrimidineColour);\r
+ colourMenu.add(tcoffeeColour);\r
colourMenu.add(userDefinedColour);\r
colourMenu.addSeparator();\r
colourMenu.add(conservationMenuItem);\r
public String getSequenceSetId() {\r
return viewport.getSequenceSetId();\r
}\r
+ \r
+ \r
+ /**\r
+ * Load the (T-Coffee) score file from the specified url \r
+ * \r
+ * @param source File/URL/T-COFFEE score file contents\r
+ * @throws IOException \r
+ * @return true if alignment was annotated with data from source\r
+ */\r
+ public boolean loadScoreFile( String source ) throws IOException {\r
+\r
+ TCoffeeScoreFile file = new TCoffeeScoreFile(source, AppletFormatAdapter.checkProtocol(source));\r
+ if( !file.isValid()) {\r
+ // TODO: raise dialog for gui\r
+ System.err.println("Problems parsing T-Coffee scores: "+file.getWarningMessage());\r
+ System.err.println("Origin was:\n"+source);\r
+ return false;\r
+ }\r
+ \r
+ /*\r
+ * check that the score matrix matches the alignment dimensions\r
+ */\r
+ AlignmentI aln; \r
+ if( (aln=viewport.getAlignment()) != null && (aln.getHeight() != file.getHeight() || aln.getWidth() != file.getWidth()) ) {\r
+ // TODO: raise a dialog box here rather than bomb out.\r
+ System.err.println("The scores matrix does not match the alignment dimensions");\r
+ \r
+ }\r
+ \r
+ // TODO add parameter to indicate if matching should be done\r
+ if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
+ {\r
+ alignPanel.fontChanged();\r
+ tcoffeeColour.setEnabled(true);\r
+ // switch to this color\r
+ changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));\r
+ return true;\r
+ } else {\r
+ System.err.println("Problems resolving T-Coffee scores:");\r
+ if (file.getWarningMessage()!=null) {\r
+ System.err.println(file.getWarningMessage());\r
+ }\r
+ }\r
+ return false;\r
+ }\r
+ \r
+ \r
}\r
git://source.jalview.org / jalview.git / blobdiff