X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=bf1481a28a24a0bebd6610351749e8ae0910892f;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=c0f85313ee804aa666ff9395e0e0ecbe0121205e;hpb=1a8f953dd71a9e319e910261927f269d69b4692c;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c0f8531..bf1481a 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,41 +1,39 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.
+ * 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 .
+ * 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.io;
-import jalview.datamodel.Alignment;
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 java.io.IOException;
+import java.util.ArrayList;
import java.util.Enumeration;
import java.util.Hashtable;
+import java.util.List;
import java.util.Vector;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.xml.sax.SAXException;
-
-import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
-import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
-import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
-import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
-
/**
* DOCUMENT ME!
*
@@ -56,7 +54,12 @@ public abstract class AlignFile extends FileParse
/**
* 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
@@ -69,13 +72,17 @@ 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();
+ // 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();
}
/**
@@ -85,17 +92,32 @@ public abstract class AlignFile extends FileParse
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
- * @throws Exception
*/
- public AlignFile(String inFile, String type) throws Exception
+ 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();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
+ if (parseImmediately)
{
- seqs.get(i).setIndex(i);
+ doParse();
}
}
@@ -104,12 +126,46 @@ public abstract class AlignFile extends FileParse
* off.
*
* @param source
- * @throws Exception
+ * @throws IOException
+ */
+ 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(FileParse source) throws Exception
+ 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++)
@@ -126,6 +182,11 @@ public abstract class AlignFile extends FileParse
return seqs;
}
+ public List getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
@@ -135,7 +196,7 @@ 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;
@@ -147,7 +208,7 @@ 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++)
@@ -159,8 +220,7 @@ public abstract class AlignFile extends FileParse
* Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
* Rna.HelixMap(pairArray);
*/
- AlignmentAnnotation an = (AlignmentAnnotation) annotations
- .elementAt(i);
+ AlignmentAnnotation an = annotations.elementAt(i);
an.validateRangeAndDisplay();
al.addAnnotation(an);
}
@@ -168,13 +228,24 @@ 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
*/
- public void addProperties(Alignment al)
+ public void addProperties(AlignmentI al)
{
if (properties != null && properties.size() > 0)
{
@@ -202,7 +273,8 @@ public abstract class AlignFile extends FileParse
if (key == null)
{
throw new Error(
- "Implementation error: Cannot have null alignment property key.");
+ MessageManager
+ .getString("error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
@@ -229,8 +301,10 @@ 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;
}
/**
@@ -241,7 +315,7 @@ public abstract class AlignFile extends FileParse
*/
protected void setSeqs(SequenceI[] s)
{
- seqs = new Vector();
+ seqs = new Vector();
for (int i = 0; i < s.length; i++)
{
@@ -251,9 +325,8 @@ public abstract class AlignFile extends FileParse
/**
* This method must be implemented to parse the contents of the file.
-
*/
- public abstract void parse() throws Exception;
+ public abstract void parse() throws IOException;
/**
* Print out in alignment file format the Sequences in the seqs Vector.
@@ -302,25 +375,29 @@ 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 });
+ newickStrings.addElement(new String[] { treeName, newickString });
}
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();
}
}