/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public abstract class AlignFile
- extends FileParse
+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 properties;
+
long start;
+
long end;
+
boolean jvSuffix = true;
/**
/**
* 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)
+ *
+ * @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
+ public AlignFile(String inFile, String type) throws IOException
{
super(inFile, type);
parse();
}
+
/**
- * Attempt to read from the position where some other parsing process left off.
+ * Attempt to read from the position where some other parsing process left
+ * off.
+ *
* @param source
* @throws IOException
*/
initData();
parse();
}
+
/**
* Return the seqs Vector
*/
return s;
}
+
/**
- * called by AppletFormatAdapter to generate
- * an annotated alignment, rather than bare
- * sequences.
+ * called by AppletFormatAdapter to generate an annotated alignment, rather
+ * than bare sequences.
+ *
* @param al
*/
public void addAnnotations(Alignment al)
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- al.addAnnotation(
- (AlignmentAnnotation) annotations.elementAt(i)
- );
+ al.addAnnotation((AlignmentAnnotation) annotations.elementAt(i));
}
}
+
/**
- * Add any additional information extracted
- * from the file to the alignment properties.
+ * Add any additional information extracted from the file to the alignment
+ * properties.
+ *
* @note implicitly called by addAnnotations()
* @param al
*/
public void addProperties(Alignment al)
{
- if (properties!=null && properties.size()>0)
+ if (properties != null && properties.size() > 0)
{
Enumeration keys = properties.keys();
Enumeration vals = properties.elements();
}
}
}
+
/**
- * Store a non-null key-value pair in a hashtable used to set alignment properties
- * note: null keys will raise an error, null values will result in the key/value pair being silently ignored.
- * @param key - non-null key object
- * @param value - non-null value
+ * Store a non-null key-value pair in a hashtable used to set alignment
+ * properties note: null keys will raise an error, null values will result in
+ * the key/value pair being silently ignored.
+ *
+ * @param key -
+ * non-null key object
+ * @param value -
+ * non-null value
*/
protected void setAlignmentProperty(Object key, Object value)
{
- if (key==null)
+ if (key == null)
{
- throw new Error("Implementation error: Cannot have null alignment property key.");
+ throw new Error(
+ "Implementation error: Cannot have null alignment property key.");
}
- if (value==null)
+ if (value == null)
{
return; // null properties are ignored.
}
- if (properties==null)
+ if (properties == null)
{
properties = new Hashtable();
}
properties.put(key, value);
}
+
protected Object getAlignmentProperty(Object key)
{
- if (properties!=null && key!=null)
+ if (properties != null && key != null)
{
return properties.get(key);
}
return null;
}
+
/**
* Initialise objects to store sequence data in.
*/
/**
* DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
protected void setSeqs(SequenceI[] s)
{
/**
* This method must be implemented to parse the contents of the file.
*/
- public abstract void parse()
- throws IOException;
+ public abstract void parse() throws IOException;
/**
* Print out in alignment file format the Sequences in the seqs Vector.
/**
* A general parser for ids.
- *
+ *
* @String id Id to be parsed
*/
Sequence parseId(String id)
}
/**
- * 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 suffix
+ * Jalview /start-end
+ *
* @String id Id to be parsed
*/
String printId(SequenceI seq)
{
return seq.getDisplayId(jvSuffix);
}
+
/**
* vector of String[] treeName, newickString pairs
*/
- Vector newickStrings=null;
+ Vector newickStrings = null;
protected void addNewickTree(String treeName, String newickString)
{
{
newickStrings = new Vector();
}
- newickStrings.addElement(new String[] { treeName, newickString});
+ newickStrings.addElement(new String[]
+ { treeName, newickString });
}
protected int getTreeCount()
{
- if (newickStrings==null)
+ if (newickStrings == null)
{
return 0;
}
git://source.jalview.org / jalview.git / blobdiff