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java.lang.ObjectIMPACT.AlignmentEditor
public class AlignmentEditor
Implementation of methods and data structures for GUIAlignmentEditor.
GUIAlignmentEditor
,
MSATableModel
Field Summary | |
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static java.lang.String |
TMPMSA_FILE
Temporary MSA file for input to PhyML. |
Constructor Summary | |
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AlignmentEditor(java.io.File file,
java.lang.String format)
Constructor method for Alignment Editor. |
Method Summary | |
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int |
getMaxTaxaNameSize()
Get maximum size for taxa name of input file read. |
int |
getSequenceCount()
Get number of sequences for file loaded. |
int |
getSiteCount()
Get number of sites for file loaded. |
java.lang.String[] |
getTableColNames()
Get column names for table. These consist of numbered sites. |
java.lang.String[] |
getTableColNamesRev()
Get column names for table. These consist of taxa names. |
java.lang.Object[][] |
getTableElements()
Get table values for table. These consist of sequences presented in rows. |
java.lang.Object[][] |
getTableElementsRev()
Get table values for table. These consist of sequences presented in columns. |
void |
initializeNormalView(boolean[] markedSeq)
Initialize normal view of data (by sequence). View can be by sequence or by site, in terms of rows. |
void |
initializeOppositeView(boolean[] markedSites)
Initialize opposite view of data (by site). View can be by sequence or by site, in terms of rows. |
boolean |
readMSAFile()
Read sequences from specified file and format. File and Format instantiated through the constructor method. |
void |
removeCanceledTMPFls(Utilities util,
java.lang.String newTreeFile,
boolean selected)
Remove temporary files created for PhyML execution resulting from cancelation. |
java.lang.String[] |
renamePhymlFiles(Utilities util,
java.lang.String newTreeFile,
boolean selected)
Rename PhyML files created on directory Phylogeny to name specified by user. |
void |
writeMSAFile(boolean[] markedSeq,
boolean[] markedSites,
java.lang.String file,
java.lang.String format)
Write sequences to specified file and format after filtering. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final java.lang.String TMPMSA_FILE
Constructor Detail |
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public AlignmentEditor(java.io.File file, java.lang.String format)
file
- The file with MSA sequence.format
- The format of file: FASTA, MASE, PHYLIP, CLUSTAL, DCSE.Method Detail |
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public int getSequenceCount()
public int getSiteCount()
public void initializeNormalView(boolean[] markedSeq)
markedSeq
- values that set selection of sequences in the table.initializeOppositeView(boolean[] markedSites)
public void initializeOppositeView(boolean[] markedSites)
markedSites
- values that set selection of sequences in the table.initializeNormalView(boolean[] markedSeq)
public java.lang.String[] getTableColNames()
MSATableModel
,
getTableElements()
,
initializeNormalView(boolean[] markedSeq)
public java.lang.Object[][] getTableElements()
MSATableModel
,
getTableColNames()
,
initializeNormalView(boolean[] markedSeq)
public java.lang.String[] getTableColNamesRev()
MSATableModel
,
getTableElementsRev()
,
initializeOppositeView(boolean[] markedSites)
public java.lang.Object[][] getTableElementsRev()
MSATableModel
,
getTableColNamesRev()
,
initializeOppositeView(boolean[] markedSites)
public int getMaxTaxaNameSize()
public boolean readMSAFile()
writeMSAFile(boolean [] markedSeq, boolean[] markedSites, String file, String format)
,
FileFormatConverter
public void writeMSAFile(boolean[] markedSeq, boolean[] markedSites, java.lang.String file, java.lang.String format)
markedSeq
- selected sequences to be written to file.markedSites
- selected sites to be written to file.file
- where to save the current table values. if null saves to currently opened file and format.format
- file format to write if saving to different file; if format null, defaults to FASTA.readMSAFile()
,
FileFormatConverter
public java.lang.String[] renamePhymlFiles(Utilities util, java.lang.String newTreeFile, boolean selected)
util
- utilities to access locations.newTreeFile
- possibly chosen by the user.selected
- true, if user chosed new tree name; false, otherwise.
public void removeCanceledTMPFls(Utilities util, java.lang.String newTreeFile, boolean selected)
util
- utilities to access locations.newTreeFile
- possibly chosen by the user.selected
- true, if user chosed new tree name; false, otherwise.
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