X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=7550a5bc8a3251e1feedde9bea716ec172321a90;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=77002cfe7afce896ffee0375659ff944d4ea569f;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 77002cf..7550a5b 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,98 +1,314 @@
-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 (Version 2.8.0b1)
+ * Copyright (C) 2014 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 <http://www.gnu.org/licenses/>.
+ * 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.Enumeration;
+import java.util.Hashtable;
+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<SequenceI> 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();
+    // sets the index of each sequence in the alignment
+    for (int i = 0, c = seqs.size(); i < c; i++)
+    {
+      seqs.get(i).setIndex(i);
+    }
+  }
+
+  /**
+   * 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();
+    // 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<SequenceI> 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++)
+    {
+      // detect if annotations.elementAt(i) rna secondary structure
+      // if so then do:
+      /*
+       * SequenceFeature[] pairArray =
+       * Rna.GetBasePairsFromAlignmentAnnotation(annotations.elementAt(i));
+       * Rna.HelixMap(pairArray);
+       */
+      AlignmentAnnotation an = (AlignmentAnnotation) annotations
+              .elementAt(i);
+      an.validateRangeAndDisplay();
+      al.addAnnotation(an);
+    }
+
+  }
+
+  /**
+   * 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();
+  }
+
+}