X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FAlignFile.java;h=977cb253dd39d8e41f10723ad0a802b5a354544c;hb=refs%2Fheads%2Ffeatures%2FJAL-1499;hp=df9d535aa1045354d18cdae3746fe15666f9a949;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
old mode 100755
new mode 100644
index df9d535..977cb25
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,179 +1,331 @@
-/*
-* 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.aaHash.containsKey(
- String.valueOf(sequence.charAt(i))))
- {
- 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 2.8.2)
+ * 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 .
+ * 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.Map;
+import java.util.Set;
+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;
+
+ /**
+ * Properties to be added to generated alignment object
+ */
+ protected Hashtable