X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=3b46760719f3e964ef5274c2c9510166ad9de37e;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=3ca2563b1e80d83ce47c28a1e0fb1510090c406c;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 3ca2563..3b46760 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,27 +1,38 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * This program 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 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
-import jalview.datamodel.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
/**
* DOCUMENT ME!
@@ -38,12 +49,17 @@ public abstract class AlignFile extends FileParse
/**
* Sequences to be added to form a new alignment.
*/
- protected Vector seqs;
+ protected Vector seqs;
/**
* annotation to be added to generated alignment object
*/
- protected Vector annotations;
+ protected Vector annotations;
+
+ /**
+ * SequenceGroups to be added to the alignment object
+ */
+ protected List seqGroups;
/**
* Properties to be added to generated alignment object
@@ -56,30 +72,51 @@ public abstract class AlignFile extends FileParse
boolean jvSuffix = true;
+ private boolean parseCalled;
+
/**
* Creates a new AlignFile object.
*/
public AlignFile()
{
+ // Shouldn't we init data structures (JBPNote: not sure - initData is for
+ // initialising the structures used for reading from a datasource, and the
+ // bare constructor hasn't got any datasource)
+ initData();
}
/**
* Constructor which parses the data from a file of some specified type.
*
* @param inFile
- * Filename to read from.
+ * Filename to read from.
* @param type
- * What type of file to read from (File, URL)
+ * What type of file to read from (File, URL)
*/
public AlignFile(String inFile, String type) throws IOException
{
+ this(true, inFile, type);
+ }
+
+ /**
+ * Constructor which (optionally delays) parsing of data from a file of some specified type.
+ *
+ * @param parseImmediately
+ * if false, need to call 'doParse()' to begin parsing data
+ * @param inFile
+ * Filename to read from.
+ * @param type
+ * What type of file to read from (File, URL)
+ * @throws IOException
+ */
+ public AlignFile(boolean parseImmediately, String inFile, String type) throws IOException
+ {
super(inFile, type);
-
initData();
-
- parse();
+ if (parseImmediately) {
+ doParse();
+ }
}
-
/**
* Attempt to read from the position where some other parsing process left
* off.
@@ -89,19 +126,58 @@ public abstract class AlignFile extends FileParse
*/
public AlignFile(FileParse source) throws IOException
{
+ this(true,source);
+ }
+ /**
+ * Construct a new parser to read from the position where some other parsing process left
+ *
+ * @param parseImmediately
+ * if false, need to call 'doParse()' to begin parsing data
+ * @param source
+ */
+ public AlignFile(boolean parseImmediately, FileParse source) throws IOException
+ {
super(source);
initData();
+ if (parseImmediately) {
+ doParse();
+ }
+ }
+ /**
+ * called if parsing was delayed till after parser was constructed
+ * @throws IOException
+ */
+ public void doParse() throws IOException
+ {
+ if (parseCalled)
+ {
+ throw new IOException(
+ "Implementation error: Parser called twice for same data.\n"
+ + "Need to call initData() again before parsing can be reattempted.");
+ }
+ parseCalled=true;
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
*/
- public Vector getSeqs()
+ public Vector getSeqs()
{
return seqs;
}
+ public List getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
@@ -111,7 +187,7 @@ public abstract class AlignFile extends FileParse
for (int i = 0; i < seqs.size(); i++)
{
- s[i] = (SequenceI) seqs.elementAt(i);
+ s[i] = seqs.elementAt(i);
}
return s;
@@ -123,24 +199,45 @@ public abstract class AlignFile extends FileParse
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
+ // detect if annotations.elementAt(i) rna secondary structure
+ // if so then do:
+ /*
+ * SequenceFeature[] pairArray =
+ * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+ * Rna.HelixMap(pairArray);
+ */
+ AlignmentAnnotation an = annotations
+ .elementAt(i);
+ an.validateRangeAndDisplay();
+ al.addAnnotation(an);
}
}
/**
+ * 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
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
@@ -158,17 +255,16 @@ public abstract class AlignFile extends FileParse
* properties note: null keys will raise an error, null values will result in
* the key/value pair being silently ignored.
*
- * @param key -
- * non-null key object
- * @param value -
- * non-null value
+ * @param key
+ * - non-null key object
+ * @param value
+ * - non-null value
*/
protected void setAlignmentProperty(Object key, Object value)
{
if (key == null)
{
- throw new Error(
- "Implementation error: Cannot have null alignment property key.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
@@ -195,19 +291,21 @@ public abstract class AlignFile extends FileParse
*/
protected void initData()
{
- seqs = new Vector();
- annotations = new Vector();
+ seqs = new Vector();
+ annotations = new Vector();
+ seqGroups = new ArrayList();
+ parseCalled=false;
}
/**
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
protected void setSeqs(SequenceI[] s)
{
- seqs = new Vector();
+ seqs = new Vector();
for (int i = 0; i < s.length; i++)
{
@@ -267,13 +365,13 @@ public abstract class AlignFile extends FileParse
/**
* vector of String[] treeName, newickString pairs
*/
- Vector newickStrings = null;
+ Vector newickStrings = null;
protected void addNewickTree(String treeName, String newickString)
{
if (newickStrings == null)
{
- newickStrings = new Vector();
+ newickStrings = new Vector();
}
newickStrings.addElement(new String[]
{ treeName, newickString });
@@ -281,11 +379,16 @@ public abstract class AlignFile extends FileParse
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();
}
}