X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=b30fe3380b264ce8832fbae52291fe45bcfaaf04;hb=552acd59bb94adcb4b8f6012a0ecb64d05c799cd;hp=da09590f9e6b8b5ba02c65b0940ed6f746875eca;hpb=04437971157c6610b64d8facea3c8028aca7927e;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index da09590..b30fe33 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,125 +1,293 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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
+ * 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.
- *
- * 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 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 java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
-import jalview.datamodel.*;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile
- extends FileParse
+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;
+ 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;
+
+ /**
+ * @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();
+ }
+
+ 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 What type of file to read from (File, URL)
+ *
+ * @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(String inFile, String type)
- throws IOException
+ public AlignFile(String dataObject, DataSourceType sourceType)
+ throws IOException
{
- super(inFile, type);
+ 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 IOException
+ */
+ public AlignFile(boolean parseImmediately, String dataObject,
+ DataSourceType sourceType) throws IOException
+ {
+ super(dataObject, sourceType);
+ initData();
+ if (parseImmediately)
+ {
+ doParse();
+ }
+ }
+
+ /**
+ * Attempt to read from the position where some other parsing process left
+ * off.
+ *
+ * @param source
+ * @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(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
+ super(source);
initData();
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+
+ if (parseImmediately)
+ {
+ 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();
+ if (closeData && !dataClosed)
+ {
+ dataIn.close();
+ dataClosed = true;
+ }
}
/**
* 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
*/
+ @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;
}
+
/**
- * called by AppletFormatAdapter to generate
- * an annotated alignment, rather than bare
- * sequences.
+ * called by AppletFormatAdapter to generate an annotated alignment, rather
+ * than bare sequences.
+ *
* @param al
*/
- public void addAnnotations(Alignment al)
+ @Override
+ 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);
}
}
+
/**
- * Add any additional information extracted
- * from the file to the alignment properties.
+ * 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)
+ if (properties != null && properties.size() > 0)
{
Enumeration keys = properties.keys();
Enumeration vals = properties.elements();
@@ -129,53 +297,65 @@ public abstract class AlignFile
}
}
}
+
/**
- * Store a non-null key-value pair in a hashtable used to set alignment 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
+ * Store a non-null key-value pair in a hashtable used to set alignment
+ * 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
*/
protected void setAlignmentProperty(Object key, Object value)
{
- if (key==null)
+ 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)
+ if (value == null)
{
return; // null properties are ignored.
}
- if (properties==null)
+ if (properties == null)
{
properties = new Hashtable();
}
properties.put(key, value);
}
+
protected Object getAlignmentProperty(Object key)
{
- if (properties!=null && key!=null)
+ if (properties != null && key != null)
{
return properties.get(key);
}
return null;
}
+
/**
* Initialise objects to store sequence data in.
*/
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!
+ *
+ * @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++)
{
@@ -186,22 +366,11 @@ public abstract class AlignFile
/**
* This method must be implemented to parse the contents of the file.
*/
- public abstract void parse()
- throws IOException;
-
- /**
- * Print out in alignment file format the Sequences in the seqs Vector.
- */
- public abstract String print();
-
- public void addJVSuffix(boolean b)
- {
- jvSuffix = b;
- }
+ public abstract void parse() throws IOException;
/**
* A general parser for ids.
- *
+ *
* @String id Id to be parsed
*/
Sequence parseId(String id)
@@ -212,7 +381,15 @@ public abstract class AlignFile
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
{
@@ -223,37 +400,54 @@ public abstract class AlignFile
}
/**
- * 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);
+ }
}