/*\r
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)\r
* Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle\r
- * \r
+ *\r
* This file is part of Jalview.\r
- * \r
+ *\r
* Jalview is free software: you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License \r
+ * modify it under the terms of the GNU General Public License\r
* as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
- * \r
- * Jalview is distributed in the hope that it will be useful, but \r
- * WITHOUT ANY WARRANTY; without even the implied warranty \r
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ *\r
+ * Jalview is distributed in the hope that it will be useful, but\r
+ * WITHOUT ANY WARRANTY; without even the implied warranty\r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR\r
* PURPOSE. See the GNU General Public License for more details.\r
- * \r
+ *\r
* You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
package jalview.appletgui;\r
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
+import javax.xml.parsers.ParserConfigurationException;\r
+\r
+import org.xml.sax.SAXException;\r
+\r
+import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;\r
+import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;\r
+import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;\r
+\r
public class AlignFrame extends EmbmenuFrame implements ActionListener, ItemListener, KeyListener\r
{\r
public AlignmentPanel alignPanel;\r
int DEFAULT_HEIGHT = 500;\r
\r
String jalviewServletURL;\r
- \r
+\r
\r
public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet, String title, boolean embedded)\r
{\r
\r
/**\r
* Load a features file onto the alignment\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
*/\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
/**\r
* Load a features file onto the alignment\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
- { \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
+ @Override\r
public void keyPressed(KeyEvent evt)\r
{\r
if (viewport.cursorMode\r
{\r
case 27: // escape key\r
deselectAllSequenceMenuItem_actionPerformed();\r
- \r
- alignPanel.alabels.cancelDrag(); \r
+\r
+ alignPanel.alabels.cancelDrag();\r
break;\r
case KeyEvent.VK_X:\r
if (evt.isControlDown() || evt.isMetaDown())\r
\r
/**\r
* called by key handler and the hide all/show all menu items\r
- * \r
+ *\r
* @param toggleSeqs\r
* @param toggleCols\r
*/\r
}\r
}\r
\r
+ @Override\r
public void keyReleased(KeyEvent evt)\r
{\r
}\r
\r
+ @Override\r
public void keyTyped(KeyEvent evt)\r
{\r
}\r
\r
+ @Override\r
public void itemStateChanged(ItemEvent evt)\r
{\r
if (evt.getSource() == displayNonconservedMenuItem)\r
this.alignPanel.annotationPanel.repaint();\r
}\r
\r
+ @Override\r
public void actionPerformed(ActionEvent evt)\r
{\r
Object source = evt.getSource();\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
jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
\r
}\r
- \r
- public void loadScores() {\r
- //TODO\r
- \r
- }\r
\r
public String outputAnnotations(boolean displayTextbox)\r
{\r
features = "# No features visible - paste some and import them here.";\r
frimport=true;\r
}\r
- \r
+\r
CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);\r
if (frimport)\r
{\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
* TODO: JAL-1104\r
* DOCUMENT ME!\r
- * \r
+ *\r
* @param e\r
* DOCUMENT ME!\r
*/\r
/**\r
* TODO: JAL-1104\r
* DOCUMENT ME!\r
- * \r
+ *\r
* @param e\r
* DOCUMENT ME!\r
*/\r
{\r
return;\r
}\r
-\r
- if (up)\r
- {\r
- for (int i = 1; i < viewport.getAlignment().getHeight(); i++)\r
- {\r
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);\r
- if (!sg.getSequences(null).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.getAlignment().getSequenceAt(i - 1);\r
- if (sg.getSequences(null).contains(temp))\r
- {\r
- continue;\r
- }\r
-\r
- viewport.getAlignment().getSequences().setElementAt(temp, i);\r
- viewport.getAlignment().getSequences().setElementAt(seq, i - 1);\r
- }\r
- }\r
- else\r
- {\r
- for (int i = viewport.getAlignment().getHeight() - 2; i > -1; i--)\r
- {\r
- SequenceI seq = viewport.getAlignment().getSequenceAt(i);\r
- if (!sg.getSequences(viewport.getHiddenRepSequences()).contains(seq))\r
- {\r
- continue;\r
- }\r
-\r
- SequenceI temp = viewport.getAlignment().getSequenceAt(i + 1);\r
- if (sg.getSequences(viewport.getHiddenRepSequences()).contains(temp))\r
- {\r
- continue;\r
- }\r
-\r
- viewport.getAlignment().getSequences().setElementAt(temp, i);\r
- viewport.getAlignment().getSequences().setElementAt(seq, i + 1);\r
- }\r
- }\r
-\r
+ viewport.getAlignment().moveSelectedSequencesByOne(sg, up ? null : viewport.getHiddenRepSequences(), up);\r
alignPanel.paintAlignment(true);\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
+ seqs2[i] = invertGroup.elementAt(i);\r
\r
SlideSequencesCommand ssc;\r
if (right)\r
\r
/**\r
* group consensus toggled\r
- * \r
+ *\r
*/\r
protected void showGroupConsensus_actionPerformed()\r
{\r
\r
/*\r
* (non-Javadoc)\r
- * \r
+ *\r
* @see\r
* jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt\r
* .event.ActionEvent)\r
}\r
/*\r
* (non-Javadoc)\r
- * \r
+ *\r
* @see\r
* jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt\r
* .event.ActionEvent)\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
\r
/**\r
* create a new view derived from the current view\r
- * \r
+ *\r
* @param viewtitle\r
* @return frame for the new view\r
*/\r
}\r
\r
/**\r
- * \r
+ *\r
* @return list of feature groups on the view\r
*/\r
public String[] getFeatureGroups()\r
\r
/**\r
* get sequence feature groups that are hidden or shown\r
- * \r
+ *\r
* @param visible\r
* true is visible\r
* @return list\r
\r
/**\r
* Change the display state for the given feature groups\r
- * \r
+ *\r
* @param groups\r
* list of group strings\r
* @param state\r
overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
+ final AlignmentPanel ap=alignPanel;\r
frame.addWindowListener(new WindowAdapter()\r
{\r
+ @Override\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
- 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
/**\r
* sort the alignment using the given treePanel\r
- * \r
+ *\r
* @param treePanel\r
* tree used to sort view\r
* @param title\r
/**\r
* Do any automatic reordering of the alignment and add the necessary bits to\r
* the menu structure for the new tree\r
- * \r
+ *\r
* @param treePanel\r
* @param title\r
*/\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
+ @Override\r
public void actionPerformed(ActionEvent evt)\r
{\r
sortByTree(treePanel, title); // treePanel.getTitle());\r
}\r
});\r
- \r
+\r
treePanel.addWindowListener(new WindowAdapter()\r
{\r
+ @Override\r
public void windowOpened(WindowEvent e)\r
{\r
if (viewport.sortByTree)\r
super.windowOpened(e);\r
}\r
\r
+ @Override\r
public void windowClosing(WindowEvent e)\r
{\r
sortByTreeMenu.remove(item);\r
this.builddate = builddate;\r
}\r
\r
+ @Override\r
public void paint(Graphics g)\r
{\r
g.setColor(Color.white);\r
MenuItem loadTree = new MenuItem("Load Associated Tree ...");\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
\r
MenuItem purinePyrimidineColour = new MenuItem();\r
MenuItem RNAHelixColour = new MenuItem();\r
- \r
+\r
MenuItem userDefinedColour = new MenuItem();\r
\r
MenuItem PIDColour = new MenuItem();\r
\r
MenuItem BLOSUM62Colour = new MenuItem();\r
- \r
+\r
MenuItem tcoffeeColour = new MenuItem();\r
\r
MenuItem njTreeBlosumMenuItem = new MenuItem();\r
CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
\r
CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
- \r
+\r
CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
Menu autoAnnMenu=new Menu();\r
CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
+ @Override\r
public void actionPerformed(ActionEvent e)\r
{\r
outputText_actionPerformed(e);\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
applyAutoAnnotationSettings.setLabel("Apply to all groups");\r
applyAutoAnnotationSettings.setState(true);\r
autoAnnMenu.setLabel("Autocalculated Annotation");\r
- \r
+\r
invertColSel.addActionListener(this);\r
showColumns.addActionListener(this);\r
showSeqs.addActionListener(this);\r
fileMenu.add(inputText);\r
fileMenu.add(loadTree);\r
fileMenu.add(loadAnnotations);\r
- fileMenu.add(loadScores);\r
- \r
+\r
fileMenu.addSeparator();\r
fileMenu.add(outputTextboxMenu);\r
fileMenu.add(outputFeatures);\r
* Attach the alignFrame panels after embedding menus, if necessary. This used\r
* to be called setEmbedded, but is now creates the dropdown menus in a\r
* platform independent manner to avoid OSX/Mac menu appendage daftness.\r
- * \r
+ *\r
* @param reallyEmbedded\r
* true to attach the view to the applet area on the page rather than\r
* in a new window\r
final AlignFrame me = this;\r
viewport.applet.addFocusListener(new FocusListener()\r
{\r
- \r
+\r
@Override\r
public void focusLost(FocusEvent e)\r
{\r
if (me.viewport.applet.currentAlignFrame==me) {\r
me.viewport.applet.currentAlignFrame = null;\r
}}\r
- \r
+\r
@Override\r
public void focusGained(FocusEvent e)\r
{\r
* structures in the original jmol window. Note This method doesn't work\r
* without an additional javascript library to exchange messages between the\r
* distinct applets. See http://issues.jalview.org/browse/JAL-621\r
- * \r
+ *\r
* @param viewer\r
* JmolViewer instance\r
* @param sequenceIds\r
}\r
/**\r
* bind a pdb file to a sequence in the current view\r
- * \r
+ *\r
* @param sequenceId\r
* - sequenceId within the dataset.\r
* @param pdbEntryString\r
\r
/**\r
* modify the current selection, providing the user has not made a selection already.\r
- * @param sel - sequences from this alignment \r
+ * @param sel - sequences from this alignment\r
* @param csel - columns to be selected on the alignment\r
*/\r
public void select(SequenceGroup sel, ColumnSelection csel)\r
\r
public void scrollTo(int row, int column)\r
{\r
- alignPanel.seqPanel.scrollTo(row, column); \r
+ alignPanel.seqPanel.scrollTo(row, column);\r
}\r
public void scrollToRow(int row)\r
{\r
- alignPanel.seqPanel.scrollToRow(row); \r
+ alignPanel.seqPanel.scrollToRow(row);\r
}\r
public void scrollToColumn(int column)\r
{\r
- alignPanel.seqPanel.scrollToColumn(column); \r
+ alignPanel.seqPanel.scrollToColumn(column);\r
}\r
/**\r
* @return the alignments unique ID.\r
public String getSequenceSetId() {\r
return viewport.getSequenceSetId();\r
}\r
- \r
- \r
+\r
+\r
/**\r
- * Load the (T-Coffee) score file from the specified url \r
- * \r
- * @param url The absolute path from where download and read the score file\r
- * @throws IOException \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
+ * @throws SAXException \r
+ * @throws ParserConfigurationException \r
+ * @throws ExceptionFileFormatOrSyntax \r
+ * @throws ExceptionLoadingFailed \r
+ * @throws ExceptionPermissionDenied \r
*/\r
- public void loadScoreFile( URL url ) throws IOException {\r
- // TODO: refactor to string/standard jalview data importer\r
- TCoffeeScoreFile file = TCoffeeScoreFile.load( new InputStreamReader( url.openStream() ) );\r
- if( file == null ) {\r
- // TODO: raise a dialog box here rather than bomb out.\r
- \r
- throw new RuntimeException("The file provided does not match the T-Coffee scores file format");\r
+ public boolean loadScoreFile( String source ) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed {\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
/*\r
* check that the score matrix matches the alignment dimensions\r
*/\r
- AlignmentI aln; \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
- throw new RuntimeException("The scores matrix does not match the alignment dimensions");\r
- \r
+ System.err.println("The scores matrix does not match the alignment dimensions");\r
+\r
}\r
- \r
+\r
// TODO add parameter to indicate if matching should be done\r
if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
{\r
- tcoffeeColour.setEnabled(true);\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
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff