X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FFinder.java;h=191f6e832ae0dd24176b8705d6c65dd09cec9283;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=528046734a68d7695bf242073c4de514411c3009;hpb=9a41fb8b4495359ca25aa0bbdd1e3bc500b2cdf2;p=jalview.git
diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java
index 5280467..191f6e8 100644
--- a/src/jalview/analysis/Finder.java
+++ b/src/jalview/analysis/Finder.java
@@ -1,33 +1,82 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
public class Finder
{
/**
* Implements the search algorithms for the Find dialog box.
*/
- SearchResults searchResults;
+ SearchResultsI searchResults;
+
AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection = null;
- Vector idMatch = null;
+
+ SequenceGroup selection = null;
+
+ Vector idMatch = null;
+
boolean caseSensitive = false;
+
+ private boolean includeDescription = false;
+
boolean findAll = false;
- com.stevesoft.pat.Regex regex = null;
+
+ Regex regex = null;
+
/**
- * hold's last-searched position between calles to find(false)
+ * holds last-searched position between calls to find(false)
*/
- int seqIndex = 0, resIndex = 0;
+ int seqIndex = 0, resIndex = -1;
+
public Finder(AlignmentI alignment, SequenceGroup selection)
{
this.alignment = alignment;
this.selection = selection;
}
+ /**
+ * restart search at given sequence and residue on alignment and (optionally)
+ * contained in selection
+ *
+ * @param alignment
+ * @param selectionGroup
+ * @param seqIndex
+ * @param resIndex
+ */
public Finder(AlignmentI alignment, SequenceGroup selectionGroup,
- int seqIndex, int resIndex)
+ int seqIndex, int resIndex)
{
this(alignment, selectionGroup);
this.seqIndex = seqIndex;
@@ -41,80 +90,108 @@ public class Finder
{
searchString = searchString.toUpperCase();
}
- regex = new com.stevesoft.pat.Regex(searchString);
+ regex = new Regex(searchString);
+ regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
- idMatch = new Vector();
- Sequence seq;
+ idMatch = new Vector();
String item = null;
boolean found = false;
-
- ////// is the searchString a residue number?
- try
- {
- int res = Integer.parseInt(searchString);
- found = true;
- if (selection == null || selection.getSize() < 1)
- {
- seq = (Sequence) alignment.getSequenceAt(0);
- }
- else
- {
- seq = (Sequence) (selection.getSequenceAt(0));
- }
-
- searchResults.addResult(seq, res, res);
- hasResults = true;
- }
- catch (NumberFormatException ex)
- {
- }
-
- ///////////////////////////////////////////////
-
int end = alignment.getHeight();
+ // /////////////////////////////////////////////
+
if (selection != null)
{
- if ( (selection.getSize() < 1) ||
- ( (selection.getEndRes() - selection.getStartRes()) < 2))
+ if ((selection.getSize() < 1)
+ || ((selection.getEndRes() - selection.getStartRes()) < 2))
{
selection = null;
}
}
+ SearchResultMatchI lastm = null;
while (!found && (seqIndex < end))
{
- seq = (Sequence) alignment.getSequenceAt(seqIndex);
+ SequenceI seq = alignment.getSequenceAt(seqIndex);
- if ( (selection != null) && !selection.getSequences(null).contains(seq))
+ if ((selection != null && selection.getSize() > 0)
+ && !selection.getSequences(null).contains(seq))
{
seqIndex++;
- resIndex = 0;
+ resIndex = -1;
continue;
}
+ if (resIndex < 0)
+ {
+ resIndex = 0;
+ // test for one off matches - sequence position and sequence ID
+ // //// is the searchString a residue number?
+ try
+ {
+ int res = Integer.parseInt(searchString);
+ // possibly a residue number - check if valid for seq
+ if (seq.getEnd() >= res)
+ {
+ searchResults.addResult(seq, res, res);
+ hasResults = true;
+ // resIndex=seq.getLength();
+ // seqIndex++;
+ if (!findAll)
+ {
+ found = true;
+ break;
+ }
+ }
+ } catch (NumberFormatException ex)
+ {
+ }
+ if (regex.search(seq.getName()) && !idMatch.contains(seq))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+
+ if (isIncludeDescription() && seq.getDescription() != null
+ && regex.search(seq.getDescription())
+ && !idMatch.contains(seq))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
+ }
item = seq.getSequenceAsString();
- if(!caseSensitive)
- item = item.toUpperCase();
- if ( (selection != null) &&
- (selection.getEndRes() < alignment.getWidth() - 1))
+ if ((selection != null)
+ && (selection.getEndRes() < alignment.getWidth() - 1))
{
item = item.substring(0, selection.getEndRes() + 1);
}
- ///Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
- StringBuffer noGapsSB = new StringBuffer();
+ // /Shall we ignore gaps???? - JBPNote: Add Flag for forcing this or not
+ StringBuilder noGapsSB = new StringBuilder();
int insertCount = 0;
- Vector spaces = new Vector();
+ List spaces = new ArrayList();
for (int j = 0; j < item.length(); j++)
{
- if (!jalview.util.Comparison.isGap(item.charAt(j)))
+ if (!Comparison.isGap(item.charAt(j)))
{
noGapsSB.append(item.charAt(j));
- spaces.addElement(new Integer(insertCount));
+ spaces.add(Integer.valueOf(insertCount));
}
else
{
@@ -123,7 +200,6 @@ public class Finder
}
String noGaps = noGapsSB.toString();
-
for (int r = resIndex; r < noGaps.length(); r++)
{
@@ -131,24 +207,22 @@ public class Finder
{
resIndex = regex.matchedFrom();
- if ( (selection != null) &&
- ( (resIndex +
- Integer.parseInt(spaces.elementAt(resIndex).toString())) <
- selection.getStartRes()))
+ if ((selection != null && selection.getSize() > 0) && (resIndex
+ + spaces.get(resIndex) < 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 invalid string used, then regex has no matched to/from
+ int sres = seq.findPosition(resIndex + spaces.get(resIndex));
+ int eres = seq.findPosition(regex.matchedTo() - 1
+ + (spaces.get(regex.matchedTo() - 1)));
+ // only add result if not contained in previous result
+ if (lastm == null || (lastm.getSequence() != seq
+ || (!(lastm.getStart() <= sres
+ && lastm.getEnd() >= eres))))
+ {
+ lastm = searchResults.addResult(seq, sres, eres);
+ }
hasResults = true;
if (!findAll)
{
@@ -170,18 +244,16 @@ public class Finder
if (!found)
{
seqIndex++;
- resIndex = 0;
+ resIndex = -1;
}
}
- for (int id = 0; id < alignment.getHeight(); id++)
- {
- if (regex.search(alignment.getSequenceAt(id).getName()))
- {
- idMatch.addElement(alignment.getSequenceAt(id));
- hasResults = true;
- }
- }
+ /**
+ * We now search the Id string in the main search loop. for (int id = 0; id
+ * < alignment.getHeight(); id++) { if
+ * (regex.search(alignment.getSequenceAt(id).getName())) {
+ * idMatch.addElement(alignment.getSequenceAt(id)); hasResults = true; } }
+ */
return hasResults;
}
@@ -194,7 +266,8 @@ public class Finder
}
/**
- * @param alignment the alignment to set
+ * @param alignment
+ * the alignment to set
*/
public void setAlignment(AlignmentI alignment)
{
@@ -210,7 +283,8 @@ public class Finder
}
/**
- * @param caseSensitive the caseSensitive to set
+ * @param caseSensitive
+ * the caseSensitive to set
*/
public void setCaseSensitive(boolean caseSensitive)
{
@@ -226,7 +300,8 @@ public class Finder
}
/**
- * @param findAll the findAll to set
+ * @param findAll
+ * the findAll to set
*/
public void setFindAll(boolean findAll)
{
@@ -242,7 +317,8 @@ public class Finder
}
/**
- * @param selection the selection to set
+ * @param selection
+ * the selection to set
*/
public void setSelection(jalview.datamodel.SequenceGroup selection)
{
@@ -250,9 +326,12 @@ public class Finder
}
/**
- * @return the idMatch
+ * Returns the (possibly empty) list of matching sequences (when search
+ * includes searching sequence names)
+ *
+ * @return
*/
- public Vector getIdMatch()
+ public Vector getIdMatch()
{
return idMatch;
}
@@ -268,7 +347,7 @@ public class Finder
/**
* @return the searchResults
*/
- public SearchResults getSearchResults()
+ public SearchResultsI getSearchResults()
{
return searchResults;
}
@@ -282,7 +361,8 @@ public class Finder
}
/**
- * @param resIndex the resIndex to set
+ * @param resIndex
+ * the resIndex to set
*/
public void setResIndex(int resIndex)
{
@@ -298,10 +378,21 @@ public class Finder
}
/**
- * @param seqIndex the seqIndex to set
+ * @param seqIndex
+ * the seqIndex to set
*/
public void setSeqIndex(int seqIndex)
{
this.seqIndex = seqIndex;
}
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
}