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JAL-1807 explicit imports (jalview.analysis)
[jalview.git]
/
src
/
jalview
/
analysis
/
Finder.java
diff --git
a/src/jalview/analysis/Finder.java
b/src/jalview/analysis/Finder.java
index
edf9deb
..
3c72598
100644
(file)
--- a/
src/jalview/analysis/Finder.java
+++ b/
src/jalview/analysis/Finder.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,9
+20,15
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import java.util.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.util.Comparison;
-import jalview.datamodel.*;
+import java.util.Vector;
+
+import com.stevesoft.pat.Regex;
public class Finder
{
public class Finder
{
@@
-33,15
+39,17
@@
public class Finder
AlignmentI alignment;
AlignmentI alignment;
- jalview.datamodel.SequenceGroup selection = null;
+ SequenceGroup selection = null;
Vector idMatch = null;
boolean caseSensitive = false;
Vector idMatch = null;
boolean caseSensitive = false;
+ private boolean includeDescription = false;
+
boolean findAll = false;
boolean findAll = false;
- com.stevesoft.pat.Regex regex = null;
+ Regex regex = null;
/**
* hold's last-searched position between calles to find(false)
/**
* hold's last-searched position between calles to find(false)
@@
-78,7
+86,7
@@
public class Finder
{
searchString = searchString.toUpperCase();
}
{
searchString = searchString.toUpperCase();
}
- regex = new com.stevesoft.pat.Regex(searchString);
+ regex = new Regex(searchString);
regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
idMatch = new Vector();
regex.setIgnoreCase(!caseSensitive);
searchResults = new SearchResults();
idMatch = new Vector();
@@
-146,6
+154,19
@@
public class Finder
break;
}
}
break;
}
}
+
+ if (isIncludeDescription() && seq.getDescription() != null
+ && regex.search(seq.getDescription()))
+ {
+ idMatch.addElement(seq);
+ hasResults = true;
+ if (!findAll)
+ {
+ // stop and return the match
+ found = true;
+ break;
+ }
+ }
}
item = seq.getSequenceAsString();
}
item = seq.getSequenceAsString();
@@
-162,7
+183,7
@@
public class Finder
for (int j = 0; j < item.length(); j++)
{
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));
{
noGapsSB.append(item.charAt(j));
spaces.addElement(new Integer(insertCount));
@@
-188,7
+209,7
@@
public class Finder
{
continue;
}
{
continue;
}
-
+// if invalid string used, then regex has no matched to/from
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
int sres = seq
.findPosition(resIndex
+ Integer.parseInt(spaces.elementAt(resIndex)
@@
-287,7
+308,7
@@
public class Finder
/**
* @return the selection
*/
/**
* @return the selection
*/
- public jalview.datamodel.SequenceGroup getSelection()
+ public SequenceGroup getSelection()
{
return selection;
}
{
return selection;
}
@@
-296,7
+317,7
@@
public class Finder
* @param selection
* the selection to set
*/
* @param selection
* the selection to set
*/
- public void setSelection(jalview.datamodel.SequenceGroup selection)
+ public void setSelection(SequenceGroup selection)
{
this.selection = selection;
}
{
this.selection = selection;
}
@@
-312,7
+333,7
@@
public class Finder
/**
* @return the regex
*/
/**
* @return the regex
*/
- public com.stevesoft.pat.Regex getRegex()
+ public Regex getRegex()
{
return regex;
}
{
return regex;
}
@@
-358,4
+379,14
@@
public class Finder
{
this.seqIndex = seqIndex;
}
{
this.seqIndex = seqIndex;
}
+
+ public boolean isIncludeDescription()
+ {
+ return includeDescription;
+ }
+
+ public void setIncludeDescription(boolean includeDescription)
+ {
+ this.includeDescription = includeDescription;
+ }
}
}