|
|||||||||
| Home >> All >> org >> xmlcml >> [ legacy overview ] | PREV NEXT | ||||||||
A
- Align - class org.xmlcml.legacy.Align.
- align
- Align() - Constructor for class org.xmlcml.legacy.Align
- Align(AlignPanel) - Constructor for class org.xmlcml.legacy.Align
- AlignPane - class org.xmlcml.legacy.AlignPane.
- AlignPane() - Constructor for class org.xmlcml.legacy.AlignPane
- AlignPanel - class org.xmlcml.legacy.AlignPanel.
- align panel
- AlignPanel() - Constructor for class org.xmlcml.legacy.AlignPanel
- AlphabetMatrix - class org.xmlcml.legacy.AlphabetMatrix.
- dynamic alignment of sequences (in the general sense) based on Kruskal's description - would be better in a different package
- AlphabetMatrix() - Constructor for class org.xmlcml.legacy.AlphabetMatrix
- aas - Static variable in class org.xmlcml.legacy.TestAlign
- abort - Variable in class org.xmlcml.legacy.Section
- abortOption - Variable in class org.xmlcml.legacy.Section
- actionPerformed(ActionEvent) - Method in class org.xmlcml.legacy.FieldTarget
- actionPerformed(ActionEvent) - Method in class org.xmlcml.legacy.SectionTarget
- addField(Field) - Method in class org.xmlcml.legacy.Section
- addLine(String) - Method in class org.xmlcml.legacy.Align
- addSection(int, int) - Method in class org.xmlcml.legacy.Align
- addVector(Vector) - Method in class org.xmlcml.legacy.Align
- addVector(Vector, IntArray) - Method in class org.xmlcml.legacy.Align
- adjustSlider(AdjustmentEvent) - Method in class org.xmlcml.legacy.Align
- align - Variable in class org.xmlcml.legacy.AlignPanel
- align() - Method in class org.xmlcml.legacy.AlignPanel
- align - Variable in class org.xmlcml.legacy.Chunk
- align - Variable in class org.xmlcml.legacy.ComparePanel
- align(double) - Method in class org.xmlcml.legacy.DynamicAligner
- this does the alignment; the gap penalty should be given
- align(double) - Method in class org.xmlcml.legacy.FileAligner
- align(String, String) - Static method in class org.xmlcml.legacy.TestAlign
- alignPanel - Variable in class org.xmlcml.legacy.Align
- alignPanel - Variable in class org.xmlcml.legacy.ComparePanel
- alignPanel - Variable in class org.xmlcml.legacy.JumboScan
- alignPanels(MouseEvent) - Method in class org.xmlcml.legacy.ComparePanel
- aligner - Variable in class org.xmlcml.legacy.FileAligner
- aminoacid - Static variable in class org.xmlcml.legacy.TestAlign
- atts - Static variable in class org.xmlcml.legacy.Align
- atts - Static variable in class org.xmlcml.legacy.Field
- atts - Static variable in class org.xmlcml.legacy.Section
B
- BACKGROUND - Static variable in class org.xmlcml.legacy.Align
- BACKGROUND - Static variable in class org.xmlcml.legacy.Field
- BACKGROUND - Static variable in class org.xmlcml.legacy.Section
- BY_TYPE - Static variable in class org.xmlcml.legacy.DynamicAligner
- penalty on basis of type (e.g.
- bottomPanel - Variable in class org.xmlcml.legacy.AlignPanel
C
- Chunk - class org.xmlcml.legacy.Chunk.
- Chunk() - Constructor for class org.xmlcml.legacy.Chunk
- Chunk(Align, IntRange) - Constructor for class org.xmlcml.legacy.Chunk
- Compare - class org.xmlcml.legacy.Compare.
- Compare() - Constructor for class org.xmlcml.legacy.Compare
- ComparePanel - class org.xmlcml.legacy.ComparePanel.
- ComparePanel(int[][], AlignPanel) - Constructor for class org.xmlcml.legacy.ComparePanel
- cPanel - Variable in class org.xmlcml.legacy.JumboScan
- caret - Variable in class org.xmlcml.legacy.Align
- charCount - Variable in class org.xmlcml.legacy.Align
- chars(char, char) - Static method in class org.xmlcml.legacy.Compare
- clearHighlights() - Method in class org.xmlcml.legacy.Align
- cols - Variable in class org.xmlcml.legacy.ComparePanel
- columns - Variable in class org.xmlcml.legacy.FileAligner
- compare() - Method in class org.xmlcml.legacy.JumboScan
- cont - Variable in class org.xmlcml.legacy.DynamicAligner
- contains(Vector, Section) - Method in class org.xmlcml.legacy.Align
- contains(int) - Method in class org.xmlcml.legacy.Chunk
- createJumboScan(String, String) - Method in class org.xmlcml.legacy.AlignPanel
- currentRow - Variable in class org.xmlcml.legacy.Align
- currentXCursor - Variable in class org.xmlcml.legacy.ComparePanel
- currentY - Variable in class org.xmlcml.legacy.Align
- currentYCursor - Variable in class org.xmlcml.legacy.ComparePanel
D
- DIAG - Variable in class org.xmlcml.legacy.AlphabetMatrix
- DynamicAligner - class org.xmlcml.legacy.DynamicAligner.
- dynamic alignment of sequences (in the general sense) based on Kruskal's description - would be better in a different package
- DynamicAligner() - Constructor for class org.xmlcml.legacy.DynamicAligner
- DynamicAligner(int[][], double[][]) - Constructor for class org.xmlcml.legacy.DynamicAligner
- create a DynamicAligner from a substitution matrix
- DynamicAligner(String, String, double[][]) - Constructor for class org.xmlcml.legacy.DynamicAligner
- dataType - Variable in class org.xmlcml.legacy.Field
- dataType - Variable in class org.xmlcml.legacy.Section
- dataTypeOption - Variable in class org.xmlcml.legacy.Field
- dataTypeOption - Variable in class org.xmlcml.legacy.Section
- defalt - Variable in class org.xmlcml.legacy.Field
- defaltOption - Variable in class org.xmlcml.legacy.Field
- delete - Variable in class org.xmlcml.legacy.Field
- delete - Variable in class org.xmlcml.legacy.Section
- deleteField(Field) - Method in class org.xmlcml.legacy.Section
- deleteOption - Variable in class org.xmlcml.legacy.Field
- deleteOption - Variable in class org.xmlcml.legacy.Section
- deleteSection(Section) - Method in class org.xmlcml.legacy.Align
- dictRef - Variable in class org.xmlcml.legacy.Field
- dictRef - Variable in class org.xmlcml.legacy.Section
- dictRefOption - Variable in class org.xmlcml.legacy.Field
- dictRefOption - Variable in class org.xmlcml.legacy.Section
- display() - Method in class org.xmlcml.legacy.AlignPanel
- doc - Variable in class org.xmlcml.legacy.Align
- drawCursor(Graphics, int, int, Align, Align) - Method in class org.xmlcml.legacy.ComparePanel
- drawCursor(Graphics, Align, Align) - Method in class org.xmlcml.legacy.ComparePanel
- drawCursor(Align, Align) - Method in class org.xmlcml.legacy.JumboScan
- dump() - Method in class org.xmlcml.legacy.Align
E
- extractAlignment() - Method in class org.xmlcml.legacy.DynamicAligner
- get the two sequences as gapped arrays of integers (e.g.
- extractAlignment() - Method in class org.xmlcml.legacy.FileAligner
F
- FOREGROUND - Static variable in class org.xmlcml.legacy.Field
- FOREGROUND - Static variable in class org.xmlcml.legacy.Section
- Field - class org.xmlcml.legacy.Field.
- Field() - Constructor for class org.xmlcml.legacy.Field
- Field(Align, int, int) - Constructor for class org.xmlcml.legacy.Field
- FieldTarget - class org.xmlcml.legacy.FieldTarget.
- FieldTarget() - Constructor for class org.xmlcml.legacy.FieldTarget
- FieldTarget(Field) - Constructor for class org.xmlcml.legacy.FieldTarget
- FileAligner - class org.xmlcml.legacy.FileAligner.
- dynamic alignment of sequences (in the general sense) based on Kruskal's description - would be better in a different package
- FileAligner() - Constructor for class org.xmlcml.legacy.FileAligner
- fail - Variable in class org.xmlcml.legacy.Section
- failOption - Variable in class org.xmlcml.legacy.Section
- field - Variable in class org.xmlcml.legacy.FieldTarget
- fieldVector - Variable in class org.xmlcml.legacy.Align
- fieldVector - Variable in class org.xmlcml.legacy.Section
- fileName - Variable in class org.xmlcml.legacy.Align
- fileString - Variable in class org.xmlcml.legacy.FileAligner
- fillMatrices(double, int) - Method in class org.xmlcml.legacy.DynamicAligner
- firstLine - Variable in class org.xmlcml.legacy.Section
- fixed - Variable in class org.xmlcml.legacy.Field
- fixedOption - Variable in class org.xmlcml.legacy.Field
- forbidScrollEvent - Variable in class org.xmlcml.legacy.Align
G
- GAP0 - Variable in class org.xmlcml.legacy.FileAligner
- gap - Static variable in class org.xmlcml.legacy.TestAlign
- getComponent() - Method in class org.xmlcml.legacy.Align
- getCurrentLine() - Method in class org.xmlcml.legacy.Align
- getCurrentYValue() - Method in class org.xmlcml.legacy.Align
- getDistance() - Method in class org.xmlcml.legacy.DynamicAligner
- return the distance between the two sequences (i.e.
- getField(int) - Method in class org.xmlcml.legacy.Section
- getInts(String, String) - Static method in class org.xmlcml.legacy.DynamicAligner
- getLineHeight() - Method in class org.xmlcml.legacy.Align
- getLock(JCheckBox) - Method in class org.xmlcml.legacy.AlignPanel
- getMatrix() - Method in class org.xmlcml.legacy.AlphabetMatrix
- getMaximumLine() - Method in class org.xmlcml.legacy.Align
- getPAM(int, int) - Static method in class org.xmlcml.legacy.TestAlign
- getScrollableTracksViewportWidth() - Method in class org.xmlcml.legacy.AlignPane
- getSection(int) - Method in class org.xmlcml.legacy.Align
- getVectorFromFile(String) - Method in class org.xmlcml.legacy.Align
- getWindowHeightInLines() - Method in class org.xmlcml.legacy.Align
H
- highlightFields() - Method in class org.xmlcml.legacy.Section
- highlightSections() - Method in class org.xmlcml.legacy.Align
- highlightSelection(AttributeSet, int, int) - Method in class org.xmlcml.legacy.Align
I
- INDIVIDUAL - Static variable in class org.xmlcml.legacy.DynamicAligner
- penalty on basis of score (e.g.
- initPane() - Method in class org.xmlcml.legacy.Align
- insertString(String) - Method in class org.xmlcml.legacy.Align
J
- JumboScan - class org.xmlcml.legacy.JumboScan.
- jumboscan
- JumboScan() - Constructor for class org.xmlcml.legacy.JumboScan
- JumboScan(AlignPanel) - Constructor for class org.xmlcml.legacy.JumboScan
- jFrame - Variable in class org.xmlcml.legacy.AlignPanel
- jScrollPane - Variable in class org.xmlcml.legacy.Align
- jumboScan - Variable in class org.xmlcml.legacy.AlignPanel
L
- LEFT - Static variable in class org.xmlcml.legacy.AlignPanel
- LEFT - Static variable in class org.xmlcml.legacy.ComparePanel
- LEFT - Static variable in class org.xmlcml.legacy.DynamicAligner
- LEFT - Static variable in class org.xmlcml.legacy.TestAlign
- Line - class org.xmlcml.legacy.Line.
- Line(Align, String, int, int) - Constructor for class org.xmlcml.legacy.Line
- lFile - Variable in class org.xmlcml.legacy.JumboScan
- lSize - Variable in class org.xmlcml.legacy.JumboScan
- lStrings - Variable in class org.xmlcml.legacy.JumboScan
- lastLine - Variable in class org.xmlcml.legacy.Section
- len - Variable in class org.xmlcml.legacy.DynamicAligner
- lineCount - Variable in class org.xmlcml.legacy.Align
- lineLabel - Variable in class org.xmlcml.legacy.Align
- lineVector - Variable in class org.xmlcml.legacy.Align
- lockWindows - Variable in class org.xmlcml.legacy.AlignPanel
M
- MAXSCORE - Static variable in class org.xmlcml.legacy.Compare
- MINSCORE - Static variable in class org.xmlcml.legacy.Compare
- main(String[]) - Static method in class org.xmlcml.legacy.AlignPanel
- main(String[]) - Static method in class org.xmlcml.legacy.DynamicAligner
- main(String[]) - Static method in class org.xmlcml.legacy.FileAligner
- main(String[]) - Static method in class org.xmlcml.legacy.JumboScan
- main(String[]) - Static method in class org.xmlcml.legacy.TestAlign
- mainPanel - Variable in class org.xmlcml.legacy.Align
- mainPanel - Variable in class org.xmlcml.legacy.AlignPanel
- makeBottomPanel() - Method in class org.xmlcml.legacy.AlignPanel
- matpnt - Static variable in class org.xmlcml.legacy.TestAlign
- matrix - Variable in class org.xmlcml.legacy.AlphabetMatrix
- matrix - Variable in class org.xmlcml.legacy.ComparePanel
- matrix - Variable in class org.xmlcml.legacy.DynamicAligner
- matrix - Variable in class org.xmlcml.legacy.JumboScan
- matrix - Static variable in class org.xmlcml.legacy.TestAlign
- maxY - Variable in class org.xmlcml.legacy.Align
- message(String) - Method in class org.xmlcml.legacy.Align
- minY - Variable in class org.xmlcml.legacy.Align
N
- NALPHA - Variable in class org.xmlcml.legacy.AlphabetMatrix
- NCHAR - Static variable in class org.xmlcml.legacy.TestAlign
- NON_DIAG - Variable in class org.xmlcml.legacy.AlphabetMatrix
O
- org.xmlcml.legacy - package org.xmlcml.legacy
P
- paint(Graphics) - Method in class org.xmlcml.legacy.ComparePanel
- paintPlot - Variable in class org.xmlcml.legacy.ComparePanel
- pam - Static variable in class org.xmlcml.legacy.TestAlign
- pane - Variable in class org.xmlcml.legacy.Align
- penalties - Variable in class org.xmlcml.legacy.DynamicAligner
- penaltyMatrix - Variable in class org.xmlcml.legacy.FileAligner
- plot() - Method in class org.xmlcml.legacy.JumboScan
- pointers - Variable in class org.xmlcml.legacy.DynamicAligner
- processFieldSelection() - Method in class org.xmlcml.legacy.Align
- processSectionSelection() - Method in class org.xmlcml.legacy.Align
R
- RIGHT - Static variable in class org.xmlcml.legacy.AlignPanel
- RIGHT - Static variable in class org.xmlcml.legacy.ComparePanel
- rFile - Variable in class org.xmlcml.legacy.JumboScan
- rSize - Variable in class org.xmlcml.legacy.JumboScan
- rStrings - Variable in class org.xmlcml.legacy.JumboScan
- range - Variable in class org.xmlcml.legacy.Chunk
- readFile() - Method in class org.xmlcml.legacy.Align
- readFile(String) - Method in class org.xmlcml.legacy.Align
- readFile(int, String) - Method in class org.xmlcml.legacy.AlignPanel
- readFile(String) - Method in class org.xmlcml.legacy.FileAligner
- readFile(String) - Method in class org.xmlcml.legacy.JumboScan
- readFiles(String, String) - Method in class org.xmlcml.legacy.JumboScan
- regexpVector - Variable in class org.xmlcml.legacy.Section
- repeat - Variable in class org.xmlcml.legacy.Section
- repeatOption - Variable in class org.xmlcml.legacy.Section
- rows - Variable in class org.xmlcml.legacy.ComparePanel
- rows - Variable in class org.xmlcml.legacy.FileAligner
S
- Section - class org.xmlcml.legacy.Section.
- Section() - Constructor for class org.xmlcml.legacy.Section
- Section(Align, int, int) - Constructor for class org.xmlcml.legacy.Section
- SectionTarget - class org.xmlcml.legacy.SectionTarget.
- SectionTarget() - Constructor for class org.xmlcml.legacy.SectionTarget
- SectionTarget(Section) - Constructor for class org.xmlcml.legacy.SectionTarget
- s - Variable in class org.xmlcml.legacy.Line
- scrollBarX - Variable in class org.xmlcml.legacy.Align
- scrollBarY - Variable in class org.xmlcml.legacy.Align
- section - Variable in class org.xmlcml.legacy.SectionTarget
- sectionVector - Variable in class org.xmlcml.legacy.Align
- seq - Variable in class org.xmlcml.legacy.DynamicAligner
- setCurrentLine(int) - Method in class org.xmlcml.legacy.Align
- setCurrentYValue(int) - Method in class org.xmlcml.legacy.Align
- setFile(int, String) - Method in class org.xmlcml.legacy.ComparePanel
- setFiles(String, String) - Method in class org.xmlcml.legacy.FileAligner
- setPAM() - Static method in class org.xmlcml.legacy.TestAlign
- setPenalties(double[][]) - Method in class org.xmlcml.legacy.DynamicAligner
- setSibling(Align) - Method in class org.xmlcml.legacy.Align
- showDialog() - Method in class org.xmlcml.legacy.Field
- showDialog() - Method in class org.xmlcml.legacy.Section
- sibling - Variable in class org.xmlcml.legacy.Align
- stepY - Variable in class org.xmlcml.legacy.Align
- string(String, String) - Static method in class org.xmlcml.legacy.Compare
- stringVector - Variable in class org.xmlcml.legacy.Align
- synchronize(Align, Align) - Method in class org.xmlcml.legacy.AlignPanel
T
- TestAlign - class org.xmlcml.legacy.TestAlign.
- TestAlign() - Constructor for class org.xmlcml.legacy.TestAlign
- title - Variable in class org.xmlcml.legacy.Field
- title - Variable in class org.xmlcml.legacy.Section
- titleOption - Variable in class org.xmlcml.legacy.Field
- titleOption - Variable in class org.xmlcml.legacy.Section
- toString() - Method in class org.xmlcml.legacy.Chunk
- toXML() - Method in class org.xmlcml.legacy.Align
- toXML() - Method in class org.xmlcml.legacy.Field
- toXML() - Method in class org.xmlcml.legacy.Section
- topBox - Variable in class org.xmlcml.legacy.Align
U
- UL - Static variable in class org.xmlcml.legacy.TestAlign
- UP - Static variable in class org.xmlcml.legacy.DynamicAligner
- UP - Static variable in class org.xmlcml.legacy.TestAlign
- UPLEFT - Static variable in class org.xmlcml.legacy.DynamicAligner
_
- _g - Variable in class org.xmlcml.legacy.ComparePanel
A B C D E F G H I J L M N O P R S T U _
|
|||||||||
| Home >> All >> org >> xmlcml >> [ legacy overview ] | PREV NEXT | ||||||||