util
Class SequenceManager

java.lang.Object
  extended by util.SequenceManager

public class SequenceManager
extends java.lang.Object

This class handles marking a sequence for the alignment.


Constructor Summary
SequenceManager()
           
 
Method Summary
static void addSequence(java.lang.String sequence)
           
static void addSequenceByPosition(int position)
           
static boolean contains(java.lang.String sequence)
          Checks if a sequenceis selected
static void emptySelectedSequences()
           
static java.lang.String getLastSelected()
           
static java.lang.String getMarkedSequenceName()
          Returns the marked sequence name.
static S3DetObject getS3detobj()
           
static java.util.Vector<java.lang.String> getSelectedSequences()
           
static SequenceImpl getSequence(java.lang.String seqName, AlignObject alObj)
          Gets the sequence related with the specified name on the alignment
static boolean isEmpty()
          Checks if the selection is empty
static boolean isSelected(java.lang.String sequence)
           
static void setLastSelected(java.lang.String lastSelected)
           
static void setMarkedSequenceName(java.lang.String markedSequenceName)
          Sets the marked sequence name.
static void setS3detobj(S3DetObject s3detobj)
           
static void setSelectedSequences(java.util.Vector<java.lang.String> selectedSequences)
           
static void toggleSequence(java.lang.String sequence)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SequenceManager

public SequenceManager()
Method Detail

getMarkedSequenceName

public static java.lang.String getMarkedSequenceName()
Returns the marked sequence name.

Returns:
markedSequenceName String

setMarkedSequenceName

public static void setMarkedSequenceName(java.lang.String markedSequenceName)
Sets the marked sequence name.

Parameters:
markedSequenceName -

getSelectedSequences

public static java.util.Vector<java.lang.String> getSelectedSequences()
Returns:
the selectedSequences

setSelectedSequences

public static void setSelectedSequences(java.util.Vector<java.lang.String> selectedSequences)
Parameters:
selectedSequences - the selectedSequences to set

addSequence

public static void addSequence(java.lang.String sequence)
Parameters:
sequence - the sequence to add

toggleSequence

public static void toggleSequence(java.lang.String sequence)
Parameters:
sequence - the sequence to add

isSelected

public static boolean isSelected(java.lang.String sequence)
Parameters:
selected - the sequence to check

emptySelectedSequences

public static void emptySelectedSequences()

getS3detobj

public static S3DetObject getS3detobj()
Returns:
the s3detobj

setS3detobj

public static void setS3detobj(S3DetObject s3detobj)
Parameters:
s3detobj - the s3detobj to set

getLastSelected

public static java.lang.String getLastSelected()
Returns:
the lastSelected

setLastSelected

public static void setLastSelected(java.lang.String lastSelected)
Parameters:
lastSelected - the lastSelected to set

addSequenceByPosition

public static void addSequenceByPosition(int position)
Parameters:
position - the position of the sequencein s3detobj

contains

public static boolean contains(java.lang.String sequence)
Checks if a sequenceis selected

Parameters:
sequence - element to find
Returns:
true if the sequence is selected, false if not

isEmpty

public static boolean isEmpty()
Checks if the selection is empty

Returns:
true if the selection is empty, false if not

getSequence

public static SequenceImpl getSequence(java.lang.String seqName,
                                       AlignObject alObj)
Gets the sequence related with the specified name on the alignment

Parameters:
seqNamem - sequence element to find
alObj - alignment to search into
Returns:
if exists, the searched sequence, null if not