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=77002cfe7afce896ffee0375659ff944d4ea569f;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
old mode 100755
new mode 100644
index 77002cf..977cb25
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -1,98 +1,331 @@
-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.
+ * 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