X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFinder.java;h=8eddc062bf2d03ab4191591ecc26d8e4dd7348a7;hb=6752a167ac486ce6edb2ac0314618e2072f29cd3;hp=3161271ac7593ba3f7bea5ddcb8d2a0c3504d27a;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git
diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 3161271..8eddc06 100755
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -1,40 +1,57 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.*;
-import java.awt.event.*;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GFinder;
+import jalview.util.MessageManager;
-import javax.swing.*;
+import java.awt.event.ActionEvent;
+import java.util.Vector;
+import java.util.regex.Pattern;
+import java.util.regex.PatternSyntaxException;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.util.MessageManager;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JOptionPane;
/**
- * DOCUMENT ME!
+ * Performs the menu option for searching the alignment, for the next or all
+ * matches. If matches are found, they are highlighted, and the user has the
+ * option to create a new feature on the alignment for the matched positions.
+ *
+ * Searches can be for a simple base sequence, or may use a regular expression.
+ * Any gaps are ignored.
*
* @author $author$
* @version $Revision$
*/
public class Finder extends GFinder
{
+ private static final int HEIGHT = 110;
+
+ private static final int WIDTH = 340;
+
AlignViewport av;
AlignmentPanel ap;
@@ -48,14 +65,7 @@ public class Finder extends GFinder
SearchResults searchResults;
/**
- * Creates a new Finder object.
- *
- * @param av
- * DOCUMENT ME!
- * @param ap
- * DOCUMENT ME!
- * @param f
- * DOCUMENT ME!
+ * Creates a new Finder object with no associated viewport or panel.
*/
public Finder()
{
@@ -63,6 +73,13 @@ public class Finder extends GFinder
focusfixed = false;
}
+ /**
+ * Constructor given an associated viewport and alignment panel. Constructs
+ * and displays an internal frame where the user can enter a search string.
+ *
+ * @param viewport
+ * @param alignPanel
+ */
public Finder(AlignViewport viewport, AlignmentPanel alignPanel)
{
av = viewport;
@@ -71,16 +88,16 @@ public class Finder extends GFinder
frame = new JInternalFrame();
frame.setContentPane(this);
frame.setLayer(JLayeredPane.PALETTE_LAYER);
- Desktop.addInternalFrame(frame, "Find", 340, 110);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.find"),
+ WIDTH, HEIGHT);
textfield.requestFocus();
}
/**
- * DOCUMENT ME!
+ * Performs the 'Find Next' action.
*
* @param e
- * DOCUMENT ME!
*/
public void findNext_actionPerformed(ActionEvent e)
{
@@ -91,10 +108,9 @@ public class Finder extends GFinder
}
/**
- * DOCUMENT ME!
+ * Performs the 'Find All' action.
*
* @param e
- * DOCUMENT ME!
*/
public void findAll_actionPerformed(ActionEvent e)
{
@@ -176,10 +192,10 @@ public class Finder extends GFinder
}
/**
- * incrementally search the alignment
+ * Search the alignment for the next or all matches. If 'all matches', a
+ * dialog is shown with the number of sequence ids and subsequences matched.
*
* @param findAll
- * true means find all results and raise a dialog box
*/
void doSearch(boolean findAll)
{
@@ -187,7 +203,7 @@ public class Finder extends GFinder
String searchString = textfield.getText().trim();
- if (searchString.length() < 1)
+ if (isInvalidSearchString(searchString))
{
return;
}
@@ -237,11 +253,14 @@ public class Finder extends GFinder
// 'SelectRegion' selection
if (!haveResults)
{
- JOptionPane.showInternalMessageDialog(this, MessageManager.getString("label.finished_searching"),
- null, JOptionPane.INFORMATION_MESSAGE);
+ JOptionPane.showInternalMessageDialog(this,
+ MessageManager.getString("label.finished_searching"), null,
+ JOptionPane.INFORMATION_MESSAGE);
resIndex = -1;
seqIndex = 0;
- } else {
+ }
+ else
+ {
if (findAll)
{
// then we report the matches that were found
@@ -264,4 +283,54 @@ public class Finder extends GFinder
}
}
+
+ /**
+ * Displays an error dialog, and answers false, if the search string is
+ * invalid, else answers true.
+ *
+ * @param searchString
+ * @return
+ */
+ protected boolean isInvalidSearchString(String searchString)
+ {
+ String error = getSearchValidationError(searchString);
+ if (error == null)
+ {
+ return false;
+ }
+ JOptionPane.showInternalMessageDialog(this, error,
+ MessageManager.getString("label.invalid_search"), // $NON-NLS-1$
+ JOptionPane.ERROR_MESSAGE);
+ return true;
+ }
+
+ /**
+ * Returns an error message string if the search string is invalid, else
+ * returns null.
+ *
+ * Currently validation is limited to checking the string is not empty, and is
+ * a valid regular expression (simple searches for base sub-sequences will
+ * pass this test). Additional validations may be added in future if the
+ * search syntax is expanded.
+ *
+ * @param searchString
+ * @return
+ */
+ protected String getSearchValidationError(String searchString)
+ {
+ String error = null;
+ if (searchString == null || searchString.length() == 0)
+ {
+ error = MessageManager.getString("label.invalid_search");
+ }
+ try
+ {
+ Pattern.compile(searchString);
+ } catch (PatternSyntaxException e)
+ {
+ error = MessageManager.getString("error.invalid_regex") + ": "
+ + e.getDescription();
+ }
+ return error;
+ }
}