X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FAlignFile.java;h=b2cf26206199ccfa2f02206d224fa3528f1eca27;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=c0f85313ee804aa666ff9395e0e0ecbe0121205e;hpb=1a8f953dd71a9e319e910261927f269d69b4692c;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index c0f8531..b2cf262 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,40 +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 ($$Version-Rel$$)
+ * 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.Sequence;
-import jalview.datamodel.SequenceI;
-
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;
+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.util.StringUtils;
/**
* DOCUMENT ME!
@@ -43,59 +42,108 @@ import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
* @version $Revision$
*/
public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 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 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
*/
- protected Hashtable properties;
+ private Hashtable properties;
long start;
long end;
- boolean jvSuffix = true;
+ /**
+ * true if parse() has been called
+ */
+ private boolean parseCalled = false;
+
+ private boolean parseImmediately = true;
+
+ private boolean dataClosed = false;
+
+ private boolean doXferSettings = true;
+
+ /**
+ * @return if doParse() was called at construction time
+ */
+ protected boolean isParseImmediately()
+ {
+ return parseImmediately;
+ }
/**
* 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();
+ }
+
+ public AlignFile(SequenceI[] seqs)
+ {
+ this();
+ setSeqs(seqs);
}
/**
* Constructor which parses the data from a file of some specified type.
*
- * @param inFile
- * Filename to read from.
- * @param type
+ * @param dataObject
+ * Filename, URL or Pasted String to read from.
+ * @param sourceType
+ * What type of file to read from (File, URL, Pasted String)
+ */
+ public AlignFile(Object dataObject, DataSourceType sourceType)
+ throws IOException
+ {
+ this(true, dataObject, sourceType);
+ }
+
+ /**
+ * 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 dataObject
+ * Filename, URL or Pasted String to read from.
+ * @param sourceType
* What type of file to read from (File, URL)
- * @throws Exception
+ * @throws IOException
*/
- public AlignFile(String inFile, String type) throws Exception
+ public AlignFile(boolean parseImmediately, Object dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(inFile, type);
+ // BH allows File or String
+ super(dataObject, sourceType);
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();
}
}
@@ -104,17 +152,80 @@ public abstract class AlignFile extends FileParse
* off.
*
* @param source
- * @throws Exception
+ * @throws IOException
*/
- public AlignFile(FileParse source) throws Exception
+ public AlignFile(FileParse source, boolean doXferSettings)
+ throws IOException
+ {
+ this(true, source, true, doXferSettings);
+ }
+
+ 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
+ {
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
+ this(parseImmediately, source, closeData, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData, boolean doXferSettings) throws IOException
{
super(source);
initData();
- parse();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
+
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+ this.doXferSettings = doXferSettings;
+
+ if (parseImmediately)
{
- seqs.get(i).setIndex(i);
+ doParse(closeData);
+ }
+ }
+
+ /**
+ * called if parsing was delayed till after parser was constructed
+ *
+ * @throws IOException
+ */
+ public void doParse() throws IOException
+ {
+ doParse(true);
+ }
+
+ public void doParse(boolean closeData) 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(this.doXferSettings);
+ if (closeData && !dataClosed)
+ {
+ dataIn.close();
+ dataClosed = true;
}
}
@@ -126,16 +237,22 @@ 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
*/
+ @Override
public SequenceI[] getSeqsAsArray()
{
SequenceI[] s = new SequenceI[seqs.size()];
for (int i = 0; i < seqs.size(); i++)
{
- s[i] = (SequenceI) seqs.elementAt(i);
+ s[i] = seqs.elementAt(i);
}
return s;
@@ -147,7 +264,8 @@ public abstract class AlignFile extends FileParse
*
* @param al
*/
- public void addAnnotations(Alignment al)
+ @Override
+ public void addAnnotations(AlignmentI al)
{
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
@@ -159,8 +277,7 @@ 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 +285,24 @@ 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)
{
@@ -201,8 +329,8 @@ 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)
{
@@ -229,8 +357,10 @@ 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;
}
/**
@@ -239,9 +369,10 @@ public abstract class AlignFile extends FileParse
* @param s
* DOCUMENT ME!
*/
- protected void setSeqs(SequenceI[] s)
+ @Override
+ public void setSeqs(SequenceI[] s)
{
- seqs = new Vector();
+ seqs = new Vector();
for (int i = 0; i < s.length; i++)
{
@@ -251,18 +382,19 @@ 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.
+ * This method is only overridden by JmolParser because of its use in
+ * StructureFile to parse annotations
+ *
+ * @param doXferSettings
+ * @throws IOException
*/
- public abstract String print();
-
- public void addJVSuffix(boolean b)
+ public void parse(boolean doXferSettings) throws IOException
{
- jvSuffix = b;
+ parse();
}
/**
@@ -274,11 +406,19 @@ public abstract class AlignFile extends FileParse
{
Sequence seq = null;
id = id.trim();
- int space = id.indexOf(" ");
+ int space = StringUtils.indexOfFirstWhitespace(id);
if (space > -1)
{
seq = new Sequence(id.substring(0, space), "");
- seq.setDescription(id.substring(space + 1));
+ String desc = id.substring(space + 1);
+ seq.setDescription(desc);
+
+ /*
+ * it is tempting to parse Ensembl style gene description e.g.
+ * chromosome:GRCh38:7:140696688:140721955:1 and set the
+ * start position of the sequence, but this causes much confusion
+ * for reverse strand feature locations
+ */
}
else
{
@@ -289,38 +429,64 @@ public abstract class AlignFile extends FileParse
}
/**
- * Creates the output id. Adds prefix Uniprot format source|id And suffix
- * Jalview /start-end
+ * Creates the output id. Adds prefix Uniprot format source|id and optionally
+ * suffix Jalview /start-end
+ *
+ * @param jvsuffix
*
* @String id Id to be parsed
*/
+ String printId(SequenceI seq, boolean jvsuffix)
+ {
+ return seq.getDisplayId(jvsuffix);
+ }
+
String printId(SequenceI seq)
{
- return seq.getDisplayId(jvSuffix);
+ return printId(seq, true);
}
/**
* 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();
+ }
+
+ @Override
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
{
- return 0;
+ al.addGroup(sg);
}
- return newickStrings.size();
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
+
+ public void setDoXferSettings(boolean b)
+ {
+ doXferSettings = b;
+ }
+
+ public boolean getDoXferSettings()
+ {
+ return doXferSettings;
+ }
}