/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.datamodel.Alignment;
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;
/**
/**
* annotation to be added to generated alignment object
*/
- protected Vector annotations;
+ protected Vector<AlignmentAnnotation> annotations;
+
+ /**
+ * SequenceGroups to be added to the alignment object
+ */
+ protected List<SequenceGroup> seqGroups;
/**
* Properties to be added to generated alignment object
boolean jvSuffix = true;
+ private boolean parseCalled;
+
/**
* Creates a new AlignFile object.
*/
*/
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();
- 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);
+ if (parseImmediately) {
+ doParse();
}
}
-
/**
* Attempt to read from the position where some other parsing process left
* off.
*/
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++)
}
}
+
/**
* Return the seqs Vector
*/
return seqs;
}
+ public List<SequenceGroup> getSeqGroups()
+ {
+ return seqGroups;
+ }
+
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
}
+ public void addSeqGroups(AlignmentI al)
+ {
+ this.seqGroups = al.getGroups();
+
+ }
+
/**
* Add any additional information extracted from the file to the alignment
* properties.
{
if (key == null)
{
- throw new Error(
- "Implementation error: Cannot have null alignment property key.");
+ throw new Error(MessageManager.getString("error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
{
seqs = new Vector();
annotations = new Vector();
+ seqGroups = new ArrayList<SequenceGroup>();
+ parseCalled=false;
}
/**