/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
*/
package jalview.io;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Vector;
+
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Sequence;
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;
-
/**
* DOCUMENT ME!
*
* @version $Revision$
*/
public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 0;
/**
* Properties to be added to generated alignment object
*/
- protected Hashtable properties;
+ private Map<String, String> properties;
long start;
long end;
- boolean jvSuffix = true;
+ /**
+ * true if parse() has been called
+ */
+ private boolean parseCalled = false;
+
+ private boolean parseImmediately = true;
- private boolean parseCalled;
+ private boolean dataClosed = false;
+
+ /**
+ * @return if doParse() was called at construction time
+ */
+ protected boolean isParseImmediately()
+ {
+ return parseImmediately;
+ }
/**
* Creates a new AlignFile object.
initData();
}
+ public AlignFile(SequenceI[] seqs)
+ {
+ this();
+ setSeqs(seqs);
+ }
+
/**
* Constructor which parses the data from a file of some specified type.
*
* @param dataObject
* Filename, URL or Pasted String to read from.
- * @param type
+ * @param sourceType
* What type of file to read from (File, URL, Pasted String)
*/
- public AlignFile(String dataObject, String type) throws IOException
+ public AlignFile(Object dataObject, DataSourceType sourceType)
+ throws IOException
{
- this(true, dataObject, type);
+ this(true, dataObject, sourceType);
}
/**
* if false, need to call 'doParse()' to begin parsing data
* @param dataObject
* Filename, URL or Pasted String to read from.
- * @param type
+ * @param sourceType
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String dataObject, String type)
- throws IOException
+ public AlignFile(boolean parseImmediately, Object dataObject,
+ DataSourceType sourceType) throws IOException
{
- super(dataObject, type);
+ // BH allows File or String
+ super(dataObject, sourceType);
initData();
if (parseImmediately)
{
public AlignFile(boolean parseImmediately, FileParse source)
throws IOException
{
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
super(source);
initData();
+
+ // stash flag in case parse needs to know if it has to autoconfigure or was
+ // configured after construction
+ this.parseImmediately = parseImmediately;
+
if (parseImmediately)
{
- doParse();
+ doParse(closeData);
}
}
*/
public void doParse() throws IOException
{
+ doParse(true);
+ }
+
+ public void doParse(boolean closeData) throws IOException
+ {
if (parseCalled)
{
throw new IOException(
}
parseCalled = true;
parse();
- // sets the index of each sequence in the alignment
- for (int i = 0, c = seqs.size(); i < c; i++)
+ if (closeData && !dataClosed)
{
- seqs.get(i).setIndex(i);
+ dataIn.close();
+ dataClosed = true;
}
}
/**
* Return the Sequences in the seqs Vector as an array of Sequences
*/
+ @Override
public SequenceI[] getSeqsAsArray()
{
SequenceI[] s = new SequenceI[seqs.size()];
*
* @param al
*/
+ @Override
public void addAnnotations(AlignmentI al)
{
addProperties(al);
*/
public void addProperties(AlignmentI al)
{
- if (properties != null && properties.size() > 0)
+ if (properties != null)
{
- Enumeration keys = properties.keys();
- Enumeration vals = properties.elements();
- while (keys.hasMoreElements())
+ for (Entry<String, String> prop : properties.entrySet())
{
- al.setProperty(keys.nextElement(), vals.nextElement());
+ al.setProperty(prop.getKey(), prop.getValue());
}
}
}
* @param value
* - non-null value
*/
- protected void setAlignmentProperty(Object key, Object value)
+ protected void setAlignmentProperty(String key, String value)
{
if (key == null)
{
throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_have_null_alignment"));
+ "Implementation error: Cannot have null alignment property key.");
}
if (value == null)
{
}
if (properties == null)
{
- properties = new Hashtable();
+ properties = new Hashtable<>();
}
properties.put(key, value);
}
- protected Object getAlignmentProperty(Object key)
+ protected String getAlignmentProperty(String key)
{
if (properties != null && key != null)
{
*/
protected void initData()
{
- seqs = new Vector<SequenceI>();
- annotations = new Vector<AlignmentAnnotation>();
- seqGroups = new ArrayList<SequenceGroup>();
+ seqs = new Vector<>();
+ annotations = new Vector<>();
+ seqGroups = new ArrayList<>();
parseCalled = false;
}
* @param s
* DOCUMENT ME!
*/
- protected void setSeqs(SequenceI[] s)
+ @Override
+ public void setSeqs(SequenceI[] s)
{
- seqs = new Vector<SequenceI>();
+ seqs = new Vector<>();
for (int i = 0; i < s.length; i++)
{
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
}
/**
- * Creates the output id. Adds prefix Uniprot format source|id And suffix
- * Jalview /start-end
+ * Creates the output id. Adds prefix Uniprot format source|id and optionally
+ * suffix Jalview /start-end
+ *
+ * @param jvsuffix
*
* @String id Id to be parsed
*/
+ String printId(SequenceI seq, boolean jvsuffix)
+ {
+ return seq.getDisplayId(jvsuffix);
+ }
+
String printId(SequenceI seq)
{
- return seq.getDisplayId(jvSuffix);
+ return printId(seq, true);
}
/**
{
if (newickStrings == null)
{
- newickStrings = new Vector<String[]>();
+ newickStrings = new Vector<>();
}
newickStrings.addElement(new String[] { treeName, newickString });
}
return newickStrings == null ? 0 : newickStrings.size();
}
+ @Override
public void addGroups(AlignmentI al)
{
}
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
}
git://source.jalview.org / jalview.git / blobdiff