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Merge remote-tracking branch 'origin/Tcoffee_JAL-1065' into develop
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
a4fb830
..
3ef7210
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-17,10
+17,15
@@
*/
package jalview.io;
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
/**
* DOCUMENT ME!
/**
* DOCUMENT ME!
@@
-37,7
+42,7
@@
public abstract class AlignFile extends FileParse
/**
* Sequences to be added to form a new alignment.
*/
/**
* Sequences to be added to form a new alignment.
*/
- protected Vector seqs;
+ protected Vector<SequenceI> seqs;
/**
* annotation to be added to generated alignment object
/**
* annotation to be added to generated alignment object
@@
-73,10
+78,12
@@
public abstract class AlignFile extends FileParse
public AlignFile(String inFile, String type) throws IOException
{
super(inFile, type);
public AlignFile(String inFile, String type) throws IOException
{
super(inFile, type);
-
initData();
initData();
-
parse();
parse();
+ // sets the index of each sequence in the alignment
+ for( int i=0,c=seqs.size(); i<c; i++ ) {
+ seqs.get(i).setIndex(i);
+ }
}
/**
}
/**
@@
-91,12
+98,16
@@
public abstract class AlignFile extends FileParse
super(source);
initData();
parse();
super(source);
initData();
parse();
+ // sets the index of each sequence in the alignment
+ for( int i=0,c=seqs.size(); i<c; i++ ) {
+ seqs.get(i).setIndex(i);
+ }
}
/**
* Return the seqs Vector
*/
}
/**
* Return the seqs Vector
*/
- public Vector getSeqs()
+ public Vector<SequenceI> getSeqs()
{
return seqs;
}
{
return seqs;
}