X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=e5c8e0419c148890c24d522d19f85465c5020dca;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=0691d82d47e10dd93bb8721fb3866f8ce860a917;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 0691d82..e5c8e04 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,178 +1,403 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-* 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.
-*
-* 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
-*/
-package jalview.io;
-
-import jalview.datamodel.*;
-
-import java.io.*;
-
-import java.util.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public abstract class AlignFile extends FileParse
-{
- int noSeqs = 0;
- int maxLength = 0;
- Vector seqs;
- Vector headers;
- long start;
- long end;
- boolean jvSuffix = true;
-
- /**
- * Creates a new AlignFile object.
- */
- public AlignFile()
- {
- }
-
-
- /**
- * 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)
- */
- public AlignFile(String inFile, String type) throws IOException
- {
- super(inFile, type);
-
- initData();
-
- parse();
- }
-
- /**
- * Return the seqs Vector
- */
- public Vector getSeqs()
- {
- return seqs;
- }
-
- /**
- * Return the Sequences in the seqs Vector as an array of Sequences
- */
- public SequenceI[] getSeqsAsArray()
- {
- SequenceI[] s = new SequenceI[seqs.size()];
-
- for (int i = 0; i < seqs.size(); i++)
- {
- s[i] = (SequenceI) seqs.elementAt(i);
- }
-
- return s;
- }
-
- /**
- * Initialise objects to store sequence data in.
- */
- protected void initData()
- {
- seqs = new Vector();
- headers = new Vector();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- */
- protected void setSeqs(SequenceI[] s)
- {
- seqs = new Vector();
-
- for (int i = 0; i < s.length; i++)
- {
- seqs.addElement(s[i]);
- }
- }
-
- // Checks whether sequence is valid aa characters
- protected boolean isValidProteinSequence(String sequence)
- {
- for (int i = 0; i < sequence.length(); i++)
- if (jalview.schemes.ResidueProperties.aaIndex[sequence.charAt(i)]==-1)
- {
- invalidCharacter = sequence.charAt(i);
- return false;
- }
-
- return true;
- }
-
- char invalidCharacter;
-
- /**
- * 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;
- }
-
- /**
- * A general parser for ids.
- *
- * @String id Id to be parsed
- */
- Sequence parseId(String id)
- {
- Sequence seq = null;
- id = id.trim();
- int space = id.indexOf(" ");
- if(space>-1)
- {
- seq = new Sequence(id.substring(0, space),"");
- seq.setDescription(id.substring(space+1));
- }
- else
- {
- seq = new Sequence(id, "");
- }
-
- return seq;
- }
-
- /**
- * Creates the output id.
- * Adds prefix Uniprot format source|id
- * And suffix Jalview /start-end
- *
- * @String id Id to be parsed
- */
- String printId(SequenceI seq)
- {
- return seq.getDisplayId(jvSuffix);
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+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;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public abstract class AlignFile extends FileParse
+{
+ int noSeqs = 0;
+
+ int maxLength = 0;
+
+ /**
+ * Sequences to be added to form a new alignment.
+ */
+ protected Vector seqs;
+
+ /**
+ * annotation to be added to generated alignment object
+ */
+ 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;
+
+ long start;
+
+ long end;
+
+ 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.
+ * @param type
+ * 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();
+ 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
+ {
+ 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()
+ {
+ return seqs;
+ }
+
+ public List getSeqGroups()
+ {
+ return seqGroups;
+ }
+
+ /**
+ * Return the Sequences in the seqs Vector as an array of Sequences
+ */
+ public SequenceI[] getSeqsAsArray()
+ {
+ SequenceI[] s = new SequenceI[seqs.size()];
+
+ for (int i = 0; i < seqs.size(); i++)
+ {
+ s[i] = seqs.elementAt(i);
+ }
+
+ return s;
+ }
+
+ /**
+ * called by AppletFormatAdapter to generate an annotated alignment, rather
+ * than bare sequences.
+ *
+ * @param al
+ */
+ public void addAnnotations(AlignmentI al)
+ {
+ addProperties(al);
+ for (int i = 0; i < annotations.size(); 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(AlignmentI al)
+ {
+ if (properties != null && properties.size() > 0)
+ {
+ Enumeration keys = properties.keys();
+ Enumeration vals = properties.elements();
+ while (keys.hasMoreElements())
+ {
+ al.setProperty(keys.nextElement(), vals.nextElement());
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ throw new Error(
+ MessageManager
+ .getString("error.implementation_error_cannot_have_null_alignment"));
+ }
+ if (value == null)
+ {
+ return; // null properties are ignored.
+ }
+ if (properties == null)
+ {
+ properties = new Hashtable();
+ }
+ properties.put(key, value);
+ }
+
+ protected Object getAlignmentProperty(Object key)
+ {
+ 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();
+ seqGroups = new ArrayList();
+ parseCalled = false;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ */
+ protected void setSeqs(SequenceI[] s)
+ {
+ seqs = new Vector();
+
+ for (int i = 0; i < s.length; i++)
+ {
+ seqs.addElement(s[i]);
+ }
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * A general parser for ids.
+ *
+ * @String id Id to be parsed
+ */
+ Sequence parseId(String id)
+ {
+ Sequence seq = null;
+ id = id.trim();
+ int space = id.indexOf(" ");
+ if (space > -1)
+ {
+ seq = new Sequence(id.substring(0, space), "");
+ seq.setDescription(id.substring(space + 1));
+ }
+ else
+ {
+ seq = new Sequence(id, "");
+ }
+
+ return seq;
+ }
+
+ /**
+ * Creates the output id. Adds prefix Uniprot format source|id And suffix
+ * Jalview /start-end
+ *
+ * @String id Id to be parsed
+ */
+ String printId(SequenceI seq)
+ {
+ return seq.getDisplayId(jvSuffix);
+ }
+
+ /**
+ * vector of String[] treeName, newickString pairs
+ */
+ Vector newickStrings = null;
+
+ protected void addNewickTree(String treeName, String newickString)
+ {
+ if (newickStrings == null)
+ {
+ newickStrings = new Vector();
+ }
+ newickStrings.addElement(new String[] { treeName, newickString });
+ }
+
+ protected int getTreeCount()
+ {
+ return newickStrings == null ? 0 : newickStrings.size();
+ }
+
+ public void addGroups(AlignmentI al)
+ {
+
+ for (SequenceGroup sg : getSeqGroups())
+ {
+ al.addGroup(sg);
+ }
+ }
+
+}