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JAl-1705 ENSEMBL cDNA type cannot be queried with peptide IDs
[jalview.git]
/
src
/
jalview
/
io
/
AlignFile.java
diff --git
a/src/jalview/io/AlignFile.java
b/src/jalview/io/AlignFile.java
index
2962cb2
..
d221d37
100755
(executable)
--- a/
src/jalview/io/AlignFile.java
+++ b/
src/jalview/io/AlignFile.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
*
@@
-20,15
+20,18
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.io.IOException;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.io.IOException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
/**
import java.util.Vector;
/**
@@
-44,14
+47,20
@@
public abstract class AlignFile extends FileParse
int maxLength = 0;
/**
int maxLength = 0;
/**
- * Sequences to be added to form a new alignment.
+ * Sequences to be added to form a new alignment. TODO: remove vector in this
+ * class
*/
protected Vector<SequenceI> seqs;
/**
* annotation to be added to generated alignment object
*/
*/
protected Vector<SequenceI> seqs;
/**
* annotation to be added to generated alignment object
*/
- protected Vector annotations;
+ protected Vector<AlignmentAnnotation> annotations;
+
+ /**
+ * SequenceGroups to be added to the alignment object
+ */
+ protected List<SequenceGroup> seqGroups;
/**
* Properties to be added to generated alignment object
/**
* Properties to be added to generated alignment object
@@
-165,6
+174,11
@@
public abstract class AlignFile extends FileParse
return seqs;
}
return seqs;
}
+ public List<SequenceGroup> getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
@@
-174,7
+188,7
@@
public abstract class AlignFile extends FileParse
for (int i = 0; i < seqs.size(); i++)
{
for (int i = 0; i < seqs.size(); i++)
{
- s[i] = (SequenceI) seqs.elementAt(i);
+ s[i] = seqs.elementAt(i);
}
return s;
}
return s;
@@
-186,7
+200,7
@@
public abstract class AlignFile extends FileParse
*
* @param al
*/
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
@@
-198,7
+212,7
@@
public abstract class AlignFile extends FileParse
* Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
* Rna.HelixMap(pairArray);
*/
* Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
* Rna.HelixMap(pairArray);
*/
- AlignmentAnnotation an = (AlignmentAnnotation) annotations
+ AlignmentAnnotation an = annotations
.elementAt(i);
an.validateRangeAndDisplay();
al.addAnnotation(an);
.elementAt(i);
an.validateRangeAndDisplay();
al.addAnnotation(an);
@@
-207,13
+221,24
@@
public abstract class AlignFile extends FileParse
}
/**
}
/**
+ * register sequence groups on the alignment for **output**
+ *
+ * @param al
+ */
+ public void addSeqGroups(AlignmentI al)
+ {
+ this.seqGroups = al.getGroups();
+
+ }
+
+ /**
* Add any additional information extracted from the file to the alignment
* properties.
*
* @note implicitly called by addAnnotations()
* @param al
*/
* Add any additional information extracted from the file to the alignment
* properties.
*
* @note implicitly called by addAnnotations()
* @param al
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
{
if (properties != null && properties.size() > 0)
{
@@
-267,8
+292,9
@@
public abstract class AlignFile extends FileParse
*/
protected void initData()
{
*/
protected void initData()
{
- seqs = new Vector();
- annotations = new Vector();
+ seqs = new Vector<SequenceI>();
+ annotations = new Vector<AlignmentAnnotation>();
+ seqGroups = new ArrayList<SequenceGroup>();
parseCalled=false;
}
parseCalled=false;
}
@@
-280,7
+306,7
@@
public abstract class AlignFile extends FileParse
*/
protected void setSeqs(SequenceI[] s)
{
*/
protected void setSeqs(SequenceI[] s)
{
- seqs = new Vector();
+ seqs = new Vector<SequenceI>();
for (int i = 0; i < s.length; i++)
{
for (int i = 0; i < s.length; i++)
{
@@
-340,13
+366,13
@@
public abstract class AlignFile extends FileParse
/**
* vector of String[] treeName, newickString pairs
*/
/**
* vector of String[] treeName, newickString pairs
*/
- Vector newickStrings = null;
+ Vector<String[]> newickStrings = null;
protected void addNewickTree(String treeName, String newickString)
{
if (newickStrings == null)
{
protected void addNewickTree(String treeName, String newickString)
{
if (newickStrings == null)
{
- newickStrings = new Vector();
+ newickStrings = new Vector<String[]>();
}
newickStrings.addElement(new String[]
{ treeName, newickString });
}
newickStrings.addElement(new String[]
{ treeName, newickString });
@@
-354,11
+380,16
@@
public abstract class AlignFile extends FileParse
protected int getTreeCount()
{
protected int getTreeCount()
{
- if (newickStrings == null)
+ return newickStrings == null ? 0 : newickStrings.size();
+ }
+
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
{
{
- return 0;
+ al.addGroup(sg);
}
}
- return newickStrings.size();
}
}
}
}