/*\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.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
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 boolean parseFeaturesFile(String file, String type, boolean autoenabledisplay)\r
- { \r
+ {\r
// TODO: test if importing a features file onto an alignment which already has features with links overwrites the original links.\r
- \r
+\r
Hashtable featureLinks = new Hashtable();\r
boolean featuresFile = false;\r
try\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
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
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
/**\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
\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
\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
final AlignmentPanel ap=alignPanel;\r
frame.addWindowListener(new WindowAdapter()\r
{\r
+ @Override\r
public void windowClosing(WindowEvent e)\r
{\r
if (ap!=null) {\r
\r
cs.setConsensus(viewport.getSequenceConsensusHash());\r
\r
- } \r
+ }\r
viewport.setGlobalColourScheme(cs);\r
\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
+\r
MenuItem outputFeatures = new MenuItem("Export Features ...");\r
\r
MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\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
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
- \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
+ * 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
+ * @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 boolean loadScoreFile( String source ) throws IOException {\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
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
System.err.println("The scores matrix does not match the alignment dimensions");\r
- \r
+\r
}\r
- \r
+\r
// TODO add parameter to indicate if matching should be done\r
if (file.annotateAlignment(alignPanel.getAlignment(), false))\r
{\r
}\r
return false;\r
}\r
- \r
- \r
+\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff