X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=2ad32f0787e97f9ea99e2ca342503440a2061880;hb=3a993bbe274824870c78bd7695c42fa93908cb30;hp=77002cfe7afce896ffee0375659ff944d4ea569f;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 77002cf..2ad32f0 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,98 +1,269 @@
-package jalview.io;
-
-import jalview.datamodel.*;
-
-import java.io.*;
-import java.util.*;
-
-public abstract class AlignFile extends FileParse {
-  int noSeqs    = 0;
-  int maxLength = 0;
-
-  Vector    seqs;
-  Vector    headers;
-
-  long start;
-  long end;
-
-  public AlignFile()
-  {}
-
-  public AlignFile(String inStr) {
-    initData();
-System.out.println("is this ever called??");
-    try{
-      parse();
-    }catch(Exception ex){}
-  }
-
-/**
- * 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();
-  }
-
-  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.aaHash.containsKey(String.valueOf(sequence.charAt(i))))
-        return false;
-
-    return true;
-  }
-
-
-/**
- * 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();
-}
+/*
+ * 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
+ * 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 java.io.*;
+import java.util.*;
+
+import jalview.datamodel.*;
+
+/**
+ * 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;
+  /**
+   * Properties to be added to generated alignment object
+   */
+  protected Hashtable properties;
+  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();
+  }
+  /**
+   * Attempt to read from the position where some other parsing process left off.
+   * @param source
+   * @throws IOException
+   */
+  public AlignFile(FileParse source) throws IOException
+  {
+    super(source);
+    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;
+  }
+  /**
+   * called by AppletFormatAdapter to generate
+   * an annotated alignment, rather than bare
+   * sequences.
+   * @param al
+   */
+  public void addAnnotations(Alignment al)
+  {
+    addProperties(al);
+    for (int i = 0; i < annotations.size(); i++)
+    {
+      al.addAnnotation(
+          (AlignmentAnnotation) annotations.elementAt(i)
+          );
+    }
+
+  }
+  /**
+   * Add any additional information extracted
+   * from the file to the alignment properties.
+   * @note implicitly called by addAnnotations()
+   * @param al
+   */
+  public void addProperties(Alignment 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("Implementation error: Cannot have null alignment property key.");
+    }
+    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();
+  }
+
+  /**
+   * 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()
+  {
+    if (newickStrings==null)
+    {
+      return 0;
+    }
+    return newickStrings.size();
+  }
+
+}