X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=41abde640304e0b78f1e9e4dda9021747c845711;hb=7c12f8eb9879172c5c437143ca5eb811a8daf5c7;hp=af1888cdd28274e22d58edbe10b6d488f159c76a;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index af1888c..41abde6 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -18,318 +18,323 @@
  */
 package jalview.gui;
 
-import java.util.*;
+import jalview.datamodel.*;
+
+import jalview.jbgui.*;
 
 import java.awt.*;
 import java.awt.event.*;
+
+import java.util.*;
+
 import javax.swing.*;
 import javax.swing.event.*;
 
-import jalview.datamodel.*;
-import jalview.jbgui.*;
 
-public class Finder
-    extends GFinder
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Finder extends GFinder
 {
-  AlignViewport av;
-  AlignmentPanel ap;
-  JInternalFrame frame;
-  SuperGroup searchGroup;
-  Vector searchResults;
-  int seqIndex = 0;
-  int resIndex = 0;
-
-  public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
-  {
-    this.av = av;
-    this.ap = ap;
-    frame = f;
-
-    // all a big pain, but we need to wait until the frame is visible before the textfield can
-    // obtain the focus/////////////////////////
-    frame.addInternalFrameListener(new InternalFrameAdapter()
-    {
-      public void internalFrameOpened(InternalFrameEvent evt)
-      {
-        SwingUtilities.invokeLater(new Runnable()
-        {
-          public void run()
-          {
-            textfield.requestFocus();
-          }
-        });
-      }
-
-      public void internalFrameClosing(InternalFrameEvent evt)
-      {
-        cancel_actionPerformed(null);
-      }
-    });
-  }
-
-  public void textfield_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findNext_actionPerformed(ActionEvent e)
-  {
-    doSearch(false);
-  }
-
-  public void findAll_actionPerformed(ActionEvent e)
-  {
-    resIndex = 0;
-    seqIndex = 0;
-    doSearch(true);
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-      ap.highlightSearchResults(null);
-      ap.idPanel.highlightSearchResults(null);
-
-      // frame.setClosed(true);
-    }
-    catch (Exception ex)
+    AlignViewport av;
+    AlignmentPanel ap;
+    JInternalFrame frame;
+    int seqIndex = 0;
+    int resIndex = 0;
+
+    SearchResults searchResults;
+
+    /**
+     * Creates a new Finder object.
+     *
+     * @param av DOCUMENT ME!
+     * @param ap DOCUMENT ME!
+     * @param f DOCUMENT ME!
+     */
+    public Finder(AlignViewport av, AlignmentPanel ap, JInternalFrame f)
     {
+        this.av = av;
+        this.ap = ap;
+        frame = f;
+
+        // all a big pain, but we need to wait until the frame is visible before the textfield can
+        // obtain the focus/////////////////////////
+        frame.addInternalFrameListener(new InternalFrameAdapter()
+            {
+                public void internalFrameOpened(InternalFrameEvent evt)
+                {
+                    SwingUtilities.invokeLater(new Runnable()
+                        {
+                            public void run()
+                            {
+                                textfield.requestFocus();
+                            }
+                        });
+                }
+            });
     }
-  }
 
-  public void createNewGroup_actionPerformed(ActionEvent e)
-  {
-    Color[] newColors = new Color[24];
 
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findNext_actionPerformed(ActionEvent e)
     {
-      newColors[i] = new Color(60, 160, 115);
+        doSearch(false);
     }
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-        newColors);
-    String searchString = textfield.getText();
-
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
-
-    for (int i = 0; i < searchResults.size(); i += 3)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void findAll_actionPerformed(ActionEvent e)
     {
-      // its possible edits may have occurred since search was performed
-      // account for this here
-      SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(
-          searchResults.elementAt(i).toString()));
-      int startRes = seq.findIndex(Integer.parseInt(
-          searchResults.elementAt(i + 1).toString())) - 1;
-      int endRes = seq.findIndex(Integer.parseInt(
-          searchResults.elementAt(i + 2).toString())) - 1;
-
-      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true,
-                                           false, startRes, endRes);
-      sg.addSequence(seq);
-      av.alignment.addGroup(sg);
-      searchGroup.addGroup(sg);
+        resIndex = 0;
+        seqIndex = 0;
+        doSearch(true);
     }
 
-    ap.av.alignment.addSuperGroup(searchGroup);
-    ap.highlightSearchResults(null);
-  }
 
-  void doSearch(boolean findAll)
-  {
-    createNewGroup.setEnabled(false);
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void createNewGroup_actionPerformed(ActionEvent e)
+    {
+        JLabel label = new JLabel("Enter name of new sequence feature");
+        JTextField textinput = new JTextField(textfield.getText());
+        JPanel panel = new JPanel(new BorderLayout());
+        panel.add(label, BorderLayout.NORTH);
+        panel.add(textinput, BorderLayout.SOUTH);
 
-    String searchString = textfield.getText().toUpperCase();
+         int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+            panel, "New Sequence Feature Name",
+          JOptionPane.OK_CANCEL_OPTION );
 
-    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
+         if(reply != JOptionPane.OK_OPTION)
+           return;
 
-    searchResults = new Vector();
+        for (int i = 0; i < searchResults.getSize(); i ++ )
+        {
+            SequenceI seq = searchResults.getResultSequence(i);
 
-    int[] allResults = null;
+            SequenceFeature sf = new SequenceFeature(textinput.getText(),
+                "Search Results", null,
+                searchResults.getResultStart(i),
+               searchResults.getResultEnd(i));
 
-    Sequence seq;
-    String item = null;
-    boolean found = false;
+            ap.seqPanel.seqCanvas.getFeatureRenderer().addNewFeature(
+                textinput.getText(), new Color(60,160,115));
 
-    ////// is the searchString a residue number?
-    try
-    {
-      int res = Integer.parseInt(searchString);
-      found = true;
-
-      if (av.getSelectionGroup().getSize() > 0)
-      {
-        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
-      }
-      else
-      {
-        seq = (Sequence) av.getAlignment().getSequenceAt(0);
-      }
-
-      searchResults.add(Integer.toString(av.getAlignment().findIndex(seq)));
-      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
-      searchResults.add(Integer.toString(seq.findIndex(res) - 1));
-    }
-    catch (NumberFormatException ex)
-    {
-    }
+            seq.getDatasetSequence().addSequenceFeature(sf);
+        }
 
-    ///////////////////////////////////////////////
-    Color[] newColors = new Color[24];
+        ap.alignFrame.showSeqFeatures.setSelected(true);
+        av.showSequenceFeatures(true);
+        ap.highlightSearchResults(null);
+    }
 
-    for (int i = 0; i < 24; i++)
+    /**
+     * DOCUMENT ME!
+     *
+     * @param findAll DOCUMENT ME!
+     */
+    void doSearch(boolean findAll)
     {
-      newColors[i] = new Color(60, 160, 115);
-    }
+        createNewGroup.setEnabled(false);
 
-    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
-        newColors);
+        String searchString = textfield.getText().toUpperCase().trim();
+        if(searchString.length()<1)
+          return;
 
-    searchGroup = new SuperGroup(searchString, ucs, true, true, false);
+        com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);
 
-    int end = av.alignment.getHeight();
+        searchResults = new SearchResults();
 
-    SequenceGroup selection = av.getSelectionGroup();
+        Sequence seq;
+        String item = null;
+        boolean found = false;
 
-    if (selection != null)
-    {
-      if ( (selection.getSize() < 1) ||
-          ( (selection.getEndRes() - selection.getStartRes()) < 2))
-      {
-        selection = null;
-      }
-    }
+        ////// is the searchString a residue number?
+        try
+        {
+            int res = Integer.parseInt(searchString);
+            found = true;
+            if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
+            {
+              seq = (Sequence) av.getAlignment().getSequenceAt(0);
+            }
+            else
+            {
+              seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
+            }
+
+            searchResults.addResult(seq, res, res);
+        }
+        catch (NumberFormatException ex)
+        {
+        }
 
-    while (!found && (seqIndex < end))
-    {
-      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+        ///////////////////////////////////////////////
+        Color[] newColors = new Color[24];
 
-      if ( (selection != null) && !selection.sequences.contains(seq))
-      {
-        seqIndex++;
-        resIndex = 0;
+        for (int i = 0; i < 24; i++)
+        {
+            newColors[i] = new Color(60, 160, 115);
+        }
 
-        continue;
-      }
+        jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(newColors);
 
-      item = seq.getSequence().toUpperCase();
+      //SG  searchGroup = new SuperGroup(searchString, ucs, true, true, false);
 
-      if ( (selection != null) &&
-          (selection.getEndRes() < av.alignment.getWidth()))
-      {
-        item = item.substring(0, selection.getEndRes() + 1);
-      }
+        int end = av.alignment.getHeight();
 
-      ///Shall we ignore gaps????
-      StringBuffer noGaps = new StringBuffer();
-      int insertCount = 0;
-      Vector spaces = new Vector();
+        SequenceGroup selection = av.getSelectionGroup();
 
-      for (int j = 0; j < item.length(); j++)
-      {
-        if (!jalview.util.Comparison.isGap(item.charAt(j)))
-        {
-          noGaps.append(item.charAt(j));
-          spaces.add(new Integer(insertCount));
-        }
-        else
+        if (selection != null)
         {
-          insertCount++;
+            if ((selection.getSize() < 1) ||
+                    ((selection.getEndRes() - selection.getStartRes()) < 2))
+            {
+                selection = null;
+            }
         }
-      }
 
-      for (int r = resIndex; r < noGaps.length(); r++)
-      {
-        if (regex.searchFrom(noGaps.toString(), r))
+        while (!found && (seqIndex < end))
         {
-          resIndex = regex.matchedFrom();
-
-          if ( (selection != null) &&
-              ( (resIndex +
-                 Integer.parseInt(spaces.get(resIndex).toString())) <
-               selection.getStartRes()))
-          {
-            continue;
-          }
-
-          searchResults.add(Integer.toString(seqIndex));
-
-          int sres = seq.findPosition(resIndex +
-                                      Integer.parseInt(spaces.elementAt(
-              resIndex)
-              .toString()));
-          int eres = seq.findPosition(regex.matchedTo() - 1 +
-                                      Integer.parseInt(spaces.elementAt(regex.
-              matchedTo() -
-              1).toString()));
-
-          searchResults.addElement(sres + "");
-          searchResults.addElement(eres + "");
-
-          if (!findAll)
-          {
-            // thats enough, break and display the result
-            found = true;
-            resIndex++;
+            seq = (Sequence) av.alignment.getSequenceAt(seqIndex);
+
+            if ((selection != null) && !selection.sequences.contains(seq))
+            {
+                seqIndex++;
+                resIndex = 0;
+
+                continue;
+            }
+
+            item = seq.getSequence().toUpperCase();
+
+            if ((selection != null) &&
+                    (selection.getEndRes() < av.alignment.getWidth()-1))
+            {
+                item = item.substring(0, selection.getEndRes() + 1);
+            }
+
+            ///Shall we ignore gaps????
+            StringBuffer noGapsSB = new StringBuffer();
+            int insertCount = 0;
+            Vector spaces = new Vector();
+
+            for (int j = 0; j < item.length(); j++)
+            {
+                if (!jalview.util.Comparison.isGap(item.charAt(j)))
+                {
+                    noGapsSB.append(item.charAt(j));
+                    spaces.add(new Integer(insertCount));
+                }
+                else
+                {
+                    insertCount++;
+                }
+            }
+
+            String noGaps = noGapsSB.toString();
+
+            for (int r = resIndex; r < noGaps.length(); r++)
+            {
+
+                if (regex.searchFrom(noGaps, r))
+                {
+                    resIndex = regex.matchedFrom();
+
+                    if ((selection != null) &&
+                            ((resIndex +
+                            Integer.parseInt(spaces.get(resIndex).toString())) < selection.getStartRes()))
+                    {
+                        continue;
+                    }
+
+
+                    int sres = seq.findPosition(resIndex +
+                            Integer.parseInt(spaces.elementAt(resIndex)
+                                                   .toString()));
+                    int eres = seq.findPosition(regex.matchedTo() - 1 +
+                            Integer.parseInt(spaces.elementAt(regex.matchedTo() -
+                                    1).toString()));
+
+                    searchResults.addResult(seq, sres, eres);
+
+                    if (!findAll)
+                    {
+                        // thats enough, break and display the result
+                        found = true;
+                        resIndex++;
+
+                        break;
+                    }
+
+                    r = resIndex;
+                }
+                else
+                {
+                  break;
+                }
+            }
+
+            if (!found)
+            {
+                seqIndex++;
+                resIndex = 0;
+            }
+        }
 
-            break;
-          }
+        Vector idMatch = new Vector();
 
-          r = resIndex;
+        for (int id = 0; id < av.alignment.getHeight(); id++)
+        {
+            if (regex.search(av.alignment.getSequenceAt(id).getName()))
+            {
+                idMatch.add(av.alignment.getSequenceAt(id));
+            }
         }
-      }
-
-      if (!found)
-      {
-        seqIndex++;
-        resIndex = 0;
-      }
-    }
 
-    Vector idMatch = new Vector();
+        if ((searchResults.getSize() == 0) && (idMatch.size() > 0))
+        {
+            ap.idPanel.highlightSearchResults(idMatch);
+        }
 
-    for (int id = 0; id < av.alignment.getHeight(); id++)
-    {
-      if (regex.search(av.alignment.getSequenceAt(id).getName()))
-      {
-        idMatch.add(av.alignment.getSequenceAt(id));
-      }
-    }
 
-    if ( (searchResults.size() == 0) && (idMatch.size() > 0))
-    {
-      ap.idPanel.highlightSearchResults(idMatch);
-    }
+        int resultSize = searchResults.getSize();
 
-    if (searchResults.size() > 0)
-    {
-      allResults = new int[searchResults.size()];
+        if (searchResults.getSize() > 0)
+          createNewGroup.setEnabled(true);
+        else
+          searchResults = null;
 
-      for (int i = 0; i < searchResults.size(); i++)
-      {
-        allResults[i] = Integer.parseInt(searchResults.get(i).toString());
-      }
+        // if allResults is null, this effectively switches displaySearch flag in seqCanvas
+        ap.highlightSearchResults(searchResults);
 
-      createNewGroup.setEnabled(true);
-    }
-    else
-    {
-      JOptionPane.showInternalMessageDialog(this, "Finished searching",
-                                            null,
-                                            JOptionPane.INFORMATION_MESSAGE);
-      resIndex = 0;
-      seqIndex = 0;
-    }
+        if(!findAll && resultSize==0)
+        {
+            JOptionPane.showInternalMessageDialog(this, "Finished searching",
+                null, JOptionPane.INFORMATION_MESSAGE);
+            resIndex = 0;
+            seqIndex = 0;
+        }
 
-    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
-    ap.highlightSearchResults(allResults);
+        if (findAll)
+        {
+          String message = resultSize + " matches found.";
+          JOptionPane.showInternalMessageDialog(this, message, null,
+                                                JOptionPane.INFORMATION_MESSAGE);
+        }
 
-    if (findAll)
-    {
-      String message = (searchResults.size() / 3) + " matches found.";
-      JOptionPane.showInternalMessageDialog(this, message, null,
-                                            JOptionPane.INFORMATION_MESSAGE);
     }
-  }
 }