X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=b2f8b2b47f838b0eb40f207acb6d9a06e64fa676;hb=a40bbc57a85658544e2e5d7cc2a7596b762566dc;hp=86696d77ddaf58eaf2ea7c4a6693bab08011e9af;hpb=c5677e9860106a821a3e6e0429b20ede7b9a732a;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 86696d7..b2f8b2b 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,40 +1,40 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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;
-
/**
* DOCUMENT ME!
*
@@ -55,7 +55,12 @@ 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
@@ -68,13 +73,17 @@ 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
- 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();
}
/**
@@ -84,48 +93,79 @@ public abstract class AlignFile extends FileParse
* Filename to read from.
* @param type
* What type of file to read from (File, URL)
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionFileFormatOrSyntax
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
*/
- public AlignFile(String inFile, String type) throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
+ 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 getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
@@ -175,6 +220,12 @@ public abstract class AlignFile extends FileParse
}
+ public void addSeqGroups(AlignmentI al)
+ {
+ this.seqGroups = al.getGroups();
+
+ }
+
/**
* Add any additional information extracted from the file to the alignment
* properties.
@@ -209,8 +260,7 @@ public abstract class AlignFile extends FileParse
{
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)
{
@@ -239,6 +289,8 @@ public abstract class AlignFile extends FileParse
{
seqs = new Vector();
annotations = new Vector();
+ seqGroups = new ArrayList();
+ parseCalled=false;
}
/**
@@ -259,14 +311,8 @@ public abstract class AlignFile extends FileParse
/**
* This method must be implemented to parse the contents of the file.
- * @throws ExceptionFileFormatOrSyntax
- * @throws SAXException
- * @throws ParserConfigurationException
- * @throws ExceptionLoadingFailed
- * @throws ExceptionPermissionDenied
- * @throws InterruptedException
*/
- public abstract void parse() throws IOException, ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException;
+ public abstract void parse() throws IOException;
/**
* Print out in alignment file format the Sequences in the seqs Vector.