X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=ba112b85781dbd6ac2791d92bb9869226131f36f;hb=77ab7d6694e27575261ab58c098eee76e68c2228;hp=b20314bb8bebefe6499d12cfc19f02b17c3092c2;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b20314b..ba112b8 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -17,29 +17,109 @@
*/
package jalview.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.datatransfer.*;
-import java.awt.dnd.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-import javax.swing.event.MenuEvent;
-
-import jalview.analysis.*;
+import jalview.analysis.AAFrequency;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.Conservation;
+import jalview.analysis.CrossRef;
+import jalview.analysis.NJTree;
+import jalview.analysis.ParseProperties;
+import jalview.analysis.SequenceIdMatcher;
import jalview.bin.Cache;
-import jalview.commands.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.ws.*;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.commands.RemoveGapColCommand;
+import jalview.commands.RemoveGapsCommand;
+import jalview.commands.SlideSequencesCommand;
+import jalview.commands.TrimRegionCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentOrder;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SeqCigar;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.AlignmentProperties;
+import jalview.io.AnnotationFile;
+import jalview.io.FeaturesFile;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
+import jalview.io.HTMLOutput;
+import jalview.io.IdentifyFile;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.JnetAnnotationMaker;
+import jalview.io.NewickFile;
+import jalview.jbgui.GAlignFrame;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.NucleotideColourScheme;
+import jalview.schemes.PIDColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.ws.WSMenuEntryProviderI;
import jalview.ws.jws1.Discoverer;
import jalview.ws.jws2.Jws2Discoverer;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+import java.awt.GridLayout;
+import java.awt.Rectangle;
+import java.awt.Toolkit;
+import java.awt.datatransfer.Clipboard;
+import java.awt.datatransfer.DataFlavor;
+import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.Transferable;
+import java.awt.dnd.DnDConstants;
+import java.awt.dnd.DropTargetDragEvent;
+import java.awt.dnd.DropTargetDropEvent;
+import java.awt.dnd.DropTargetEvent;
+import java.awt.dnd.DropTargetListener;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.PrinterJob;
+import java.beans.PropertyChangeEvent;
+import java.io.File;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JEditorPane;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JLayeredPane;
+import javax.swing.JMenu;
+import javax.swing.JMenuItem;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JProgressBar;
+import javax.swing.JRadioButtonMenuItem;
+import javax.swing.JScrollPane;
+import javax.swing.SwingUtilities;
+
/**
* DOCUMENT ME!
*
@@ -675,7 +755,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
progressBars.put(lId, progressPanel);
}
// update GUI
- setMenusForViewport();
+ // setMenusForViewport();
validate();
}
@@ -1115,7 +1195,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
String choice = chooser.getSelectedFile().getPath();
jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
- loadJalviewDataFile(choice);
+ loadJalviewDataFile(choice, null, null, null);
}
}
@@ -2000,6 +2080,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
alignPanel.idPanel.idCanvas.searchResults = null;
alignPanel.paintAlignment(true);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
/**
@@ -2025,14 +2106,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
alignPanel.paintAlignment(true);
- viewport.sendSelection();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
+ viewport.sendSelection();
}
public void invertColSel_actionPerformed(ActionEvent e)
{
viewport.invertColumnSelection();
alignPanel.paintAlignment(true);
+ viewport.sendSelection();
}
/**
@@ -2243,8 +2325,57 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void newView_actionPerformed(ActionEvent e)
{
+ newView(true);
+ }
+
+ /**
+ *
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(boolean copyAnnotation)
+ {
+ return newView(null, copyAnnotation);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle)
+ {
+ return newView(viewTitle, true);
+ }
+
+ /**
+ *
+ * @param viewTitle
+ * title of newly created view
+ * @param copyAnnotation
+ * if true then duplicate all annnotation, groups and settings
+ * @return new alignment panel, already displayed.
+ */
+ public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
+ {
AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel,
true);
+ if (!copyAnnotation)
+ {
+ // just remove all the current annotation except for the automatic stuff
+ newap.av.alignment.deleteAllGroups();
+ for (AlignmentAnnotation alan : newap.av.alignment
+ .getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated)
+ {
+ newap.av.alignment.deleteAnnotation(alan);
+ }
+ ;
+ }
+ }
newap.av.gatherViewsHere = false;
@@ -2257,8 +2388,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.redoList = viewport.redoList;
int index = Desktop.getViewCount(viewport.getSequenceSetId());
- String newViewName = "View " + index;
-
+ // make sure the new view has a unique name - this is essential for Jalview
+ // 2 archives
+ boolean addFirstIndex = false;
+ if (viewTitle == null || viewTitle.trim().length() == 0)
+ {
+ viewTitle = "View";
+ addFirstIndex = true;
+ }
+ else
+ {
+ index = 1;// we count from 1 if given a specific name
+ }
+ String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
Vector comps = (Vector) PaintRefresher.components.get(viewport
.getSequenceSetId());
Vector existingNames = new Vector();
@@ -2276,7 +2418,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
while (existingNames.contains(newViewName))
{
- newViewName = "View " + (++index);
+ newViewName = viewTitle + " " + (++index);
}
newap.av.viewName = newViewName;
@@ -2288,6 +2430,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.gatherViewsHere = true;
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+ return newap;
}
public void expandViews_actionPerformed(ActionEvent e)
@@ -2663,57 +2806,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
JEditorPane editPane = new JEditorPane("text/html", "");
editPane.setEditable(false);
- StringBuffer contents = new StringBuffer("");
-
- float avg = 0;
- int min = Integer.MAX_VALUE, max = 0;
- for (int i = 0; i < viewport.alignment.getHeight(); i++)
- {
- int size = viewport.alignment.getSequenceAt(i).getEnd()
- - viewport.alignment.getSequenceAt(i).getStart();
- avg += size;
- if (size > max)
- max = size;
- if (size < min)
- min = size;
- }
- avg = avg / (float) viewport.alignment.getHeight();
-
- contents.append("
Sequences: " + viewport.alignment.getHeight());
- contents.append("
Minimum Sequence Length: " + min);
- contents.append("
Maximum Sequence Length: " + max);
- contents.append("
Average Length: " + (int) avg);
-
- if (((Alignment) viewport.alignment).getProperties() != null)
- {
- Hashtable props = ((Alignment) viewport.alignment).getProperties();
- Enumeration en = props.keys();
- contents.append("
");
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- StringBuffer val = new StringBuffer();
- String vals = props.get(key).toString();
- int pos = 0, npos;
- do
- {
- npos = vals.indexOf("\n", pos);
- if (npos == -1)
- {
- val.append(vals.substring(pos));
- }
- else
- {
- val.append(vals.substring(pos, npos));
- val.append("
");
- }
- pos = npos + 1;
- } while (npos != -1);
- contents.append("" + key + " | " + val + " |
");
- }
- contents.append("
");
- }
- editPane.setText(contents.toString() + "");
+ StringBuffer contents = new AlignmentProperties(viewport.alignment)
+ .formatAsHtml();
+ editPane.setText("" + contents.toString() + "");
JInternalFrame frame = new JInternalFrame();
frame.getContentPane().add(new JScrollPane(editPane));
@@ -3630,6 +3725,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
}
+ public boolean sortBy(AlignmentOrder alorder, String undoname)
+ {
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
+ if (undoname != null)
+ {
+ addHistoryItem(new OrderCommand(undoname, oldOrder,
+ viewport.alignment));
+ }
+ alignPanel.paintAlignment(true);
+ return true;
+ }
+
/**
* Work out whether the whole set of sequences or just the selected set will
* be submitted for multiple alignment.
@@ -3853,6 +3961,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
// object broker mechanism.
final Vector wsmenu = new Vector();
final IProgressIndicator af = me;
+ final JMenu msawsmenu = new JMenu("Alignment");
+ final JMenu secstrmenu = new JMenu(
+ "Secondary Structure Prediction");
+ final JMenu seqsrchmenu = new JMenu(
+ "Sequence Database Search");
+ final JMenu analymenu = new JMenu(
+ "Analyse Alignment");
+
if (Cache.getDefault("SHOW_JWS1_SERVICES", true)
&& Discoverer.services != null
&& (Discoverer.services.size() > 0))
@@ -3871,7 +3987,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (msaws != null)
{
// Add any Multiple Sequence Alignment Services
- final JMenu msawsmenu = new JMenu("Alignment");
for (int i = 0, j = msaws.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) msaws
@@ -3881,13 +3996,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
impl.attachWSMenuEntry(msawsmenu, me);
}
- wsmenu.add(msawsmenu);
}
if (secstrpr != null)
{
// Add any secondary structure prediction services
- final JMenu secstrmenu = new JMenu(
- "Secondary Structure Prediction");
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) secstrpr
@@ -3896,13 +4008,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getServiceClient(sh);
impl.attachWSMenuEntry(secstrmenu, me);
}
- wsmenu.add(secstrmenu);
}
if (seqsrch != null)
{
// Add any sequence search services
- final JMenu seqsrchmenu = new JMenu(
- "Sequence Database Search");
for (int i = 0, j = seqsrch.size(); i < j; i++)
{
final ext.vamsas.ServiceHandle sh = (ext.vamsas.ServiceHandle) seqsrch
@@ -3911,7 +4020,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
.getServiceClient(sh);
impl.attachWSMenuEntry(seqsrchmenu, me);
}
- wsmenu.add(seqsrchmenu);
}
}
@@ -3924,14 +4032,22 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (jws2servs.hasServices())
{
JMenu jws2men = new JMenu("Jaba Web Services");
- jws2servs.attachWSMenuEntry(jws2men, me);
- for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
- {
- wsmenu.add(jws2men.getMenuComponent(i));
- }
+ jws2servs.attachWSMenuEntry(msawsmenu, me);
+// for (int i = 0, iSize = jws2men.getMenuComponentCount(); i < iSize; i++)
+// {
+// msawsmenu.add(jws2men.getMenuComponent(i));
+// }
}
}
}
+ if (msawsmenu.getMenuComponentCount()>0)
+ wsmenu.add(msawsmenu);
+ if (secstrmenu.getMenuComponentCount()>0)
+ wsmenu.add(secstrmenu);
+ if (analymenu.getMenuComponentCount()>0)
+ wsmenu.add(analymenu);
+ if (seqsrchmenu.getMenuComponentCount()>0)
+ wsmenu.add(seqsrchmenu);
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@@ -3994,6 +4110,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
jalview.ws.EnfinEnvision2OneWay.getInstance().attachWSMenuEntry(
webService, this);
}
+ // TODO: remove this code when 2.7 is released
+ // DEBUG - alignmentView
+ /*
+ * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
+ * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
+ *
+ * @Override public void actionPerformed(ActionEvent e) {
+ * jalview.datamodel.AlignmentView.testSelectionViews(af.viewport.alignment,
+ * af.viewport.colSel, af.viewport.selectionGroup); }
+ *
+ * }); webService.add(testAlView);
+ */
+ // TODO: refactor to RestClient discoverer and merge menu entries for
+ // rest-style services with other types of analysis/calculation service
+ // SHmmr test client - still being implemented.
+
+ for (jalview.ws.rest.RestClient client: jalview.ws.rest.RestClient.getRestClients()) {
+ client.attachWSMenuEntry(JvSwingUtils.findOrCreateMenu(webService, client.getAction()), this);
+ }
+ // DEBUG - alignmentView
}
/*
@@ -4265,7 +4401,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
featuresFile = new FeaturesFile(file, type)
.parse(viewport.alignment.getDataset(),
alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours,
- false);
+ false, jalview.bin.Cache.getDefault(
+ "RELAXEDSEQIDMATCHING", false));
} catch (Exception ex)
{
ex.printStackTrace();
@@ -4360,10 +4497,127 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
{
try
{
-
+ // check to see if any of these files have names matching sequences in
+ // the alignment
+ SequenceIdMatcher idm = new SequenceIdMatcher(viewport
+ .getAlignment().getSequencesArray());
+ /**
+ * Object[] { String,SequenceI}
+ */
+ ArrayList