*/
package jalview.io;
-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.List;
import java.util.Vector;
+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 jalview.util.StringUtils;
+
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile extends FileParse implements AlignmentFileI
+public abstract class AlignFile extends FileParse
+ implements AlignmentFileReaderI, AlignmentFileWriterI
{
int noSeqs = 0;
/**
* Properties to be added to generated alignment object
*/
- protected Hashtable properties;
+ private Hashtable properties;
long start;
long end;
- boolean jvSuffix = true;
+ /**
+ * true if parse() has been called
+ */
+ private boolean parseCalled = false;
- private boolean parseCalled;
+ private boolean parseImmediately = true;
+
+ private boolean dataClosed = false;
+
+ private boolean doXferSettings = true;
+
+ /**
+ * @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 sourceType
* What type of file to read from (File, URL, Pasted String)
*/
- public AlignFile(String dataObject, DataSourceType sourceType)
+ public AlignFile(Object dataObject, DataSourceType sourceType)
throws IOException
{
this(true, dataObject, sourceType);
* What type of file to read from (File, URL)
* @throws IOException
*/
- public AlignFile(boolean parseImmediately, String dataObject,
- DataSourceType sourceType)
- throws IOException
+ public AlignFile(boolean parseImmediately, Object dataObject,
+ DataSourceType sourceType) throws IOException
{
+ // BH allows File or String
super(dataObject, sourceType);
initData();
if (parseImmediately)
* @param source
* @throws IOException
*/
+ public AlignFile(FileParse source, boolean doXferSettings)
+ throws IOException
+ {
+ this(true, source, true, doXferSettings);
+ }
+
public AlignFile(FileParse source) throws IOException
{
this(true, source);
public AlignFile(boolean parseImmediately, FileParse source)
throws IOException
{
+ this(parseImmediately, source, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData) throws IOException
+ {
+ this(parseImmediately, source, closeData, true);
+ }
+
+ public AlignFile(boolean parseImmediately, FileParse source,
+ boolean closeData, boolean doXferSettings) 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;
+ this.doXferSettings = doXferSettings;
+
if (parseImmediately)
{
- doParse();
+ doParse(closeData);
}
}
*/
public void doParse() throws IOException
{
+ doParse(true);
+ }
+
+ public void doParse(boolean closeData) throws IOException
+ {
if (parseCalled)
{
throw new IOException(
+ "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++)
+ parse(this.doXferSettings);
+ if (closeData && !dataClosed)
{
- seqs.get(i).setIndex(i);
+ dataIn.close();
+ dataClosed = true;
}
}
{
if (key == null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_cannot_have_null_alignment"));
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_cannot_have_null_alignment"));
}
if (value == null)
{
public abstract void parse() throws IOException;
/**
- * Print out in alignment file format the Sequences in the seqs Vector.
+ * This method is only overridden by JmolParser because of its use in
+ * StructureFile to parse annotations
+ *
+ * @param doXferSettings
+ * @throws IOException
*/
- @Override
- public abstract String print();
-
- @Override
- public void addJVSuffix(boolean b)
+ public void parse(boolean doXferSettings) throws IOException
{
- jvSuffix = b;
+ parse();
}
/**
{
Sequence seq = null;
id = id.trim();
- int space = id.indexOf(" ");
+ int space = StringUtils.indexOfFirstWhitespace(id);
if (space > -1)
{
seq = new Sequence(id.substring(0, space), "");
}
/**
- * 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);
}
/**
}
}
+ protected void addSequence(SequenceI seq)
+ {
+ seqs.add(seq);
+ }
+
+ public void setDoXferSettings(boolean b)
+ {
+ doXferSettings = b;
+ }
+
+ public boolean getDoXferSettings()
+ {
+ return doXferSettings;
+ }
}
git://source.jalview.org / jalview.git / blobdiff