|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object charite.christo.strap.ResidueAnnotation
public final class ResidueAnnotation
HELP Residue annotations, allow the assignment of information to specific amino acids or nucleotides of proteins. They are special types of residue selections. A residue annotation has a list of entries each having a type, modifiable text. The user can change these entries and add new entries. Depending on the type, the entries contain different information:
Nested Class Summary | |
---|---|
static class |
ResidueAnnotation.Entry
|
Field Summary | |
---|---|
static java.lang.String |
ATOMS
|
static java.lang.String |
BALLOON
|
static java.lang.String |
BG_IMAGE
|
static java.lang.String |
COLOR
|
static java.lang.String |
DISABLED
|
static long |
ENTRY_NOT_SAVED
|
static java.lang.String |
GROUP
|
static java.lang.String |
HYPERREFS
|
static java.lang.String[] |
MAIN_KEYS
|
static java.lang.String |
NAME
|
static ResidueAnnotation[] |
NONE
|
static java.lang.String[] |
OTHER_KEYS
|
static java.lang.String |
POS
|
static java.lang.String |
SPECIFIC_VIEW3D
|
static java.lang.String |
STYLE
|
static java.lang.String |
TEXSHADE
|
static java.lang.String |
VIEW3D
|
Fields inherited from interface charite.christo.protein.ResidueSelection |
---|
NAME_BACKBONE, NAME_CURSOR, NAME_MOUSE_OVER, NAME_STANDARD |
Fields inherited from interface charite.christo.protein.VisibleIn123 |
---|
ANYWHERE, ARROW_HEADS, BIT_SHIFT_LINE, HTML, JALVIEW, NO_FLASH, SB, SEQUENCE, STRUCTURE, STYLE_BACKGROUND, STYLE_CIRCLE, STYLE_CURSOR, STYLE_DOTTED, STYLE_HIDDEN, STYLE_IMAGE, STYLE_IMAGE_LUCID, STYLE_LOWER_HALF_BACKGROUND, STYLE_UNDERLINE, STYLE_UPPER_HALF_BACKGROUND |
Fields inherited from interface charite.christo.HasRenderer |
---|
JLIST, STRIKE_THROUGH |
Fields inherited from interface charite.christo.ChRunnable |
---|
APPEND, COLUMN_TITLE, DOWNLOAD_FINISHED, GET_PANEL, ICON, INTERPRET_LINE, IS_DRAG4XY, ITEM_TEXT, MODIFY_RENDERER_COMPONENT, PROGRESS, REPAINT_CURSOR, SAY_DOWNLOADING, SET_ICON_IMAGE, SET_TREE_VALUE, SHOW_IN_FRAME, TAB_TEXT, TIP_TEXT |
Constructor Summary | |
---|---|
ResidueAnnotation(Protein p)
|
Method Summary | |
---|---|
void |
addE(long options,
java.lang.String key,
java.lang.String value,
boolean isEnabled,
int row)
|
void |
addE(java.lang.String key0,
java.lang.String value)
|
void |
addEnS(java.lang.String key0,
java.lang.String value)
|
void |
dispose()
|
boolean |
featureEndsWithAminoName()
|
java.awt.Color |
getColor()
|
java.lang.String |
getCssClass()
|
ResidueAnnotation.Entry[] |
getEntries()
|
java.lang.String |
getFeatureName()
|
javax.swing.ImageIcon |
getIcon()
|
java.lang.String |
getID()
|
java.awt.Image |
getImage(java.awt.Component observer)
|
java.lang.String |
getName()
A ResidueAnnotation-object has a name. |
java.util.Map |
getPropertyMap(boolean create)
|
Protein |
getProtein()
ResidueAnnotation-Objects belong to a certain protein |
java.lang.Object |
getRenderer(long options,
long[] rendOptions)
|
long |
getRendererModiCount()
|
boolean[] |
getSelectedAminoacids()
|
int |
getSelectedAminoacidsOffset()
|
boolean[] |
getSelectedNucleotides()
|
int |
getSelectedNucleotidesOffset()
The goal is to reduce the size of the returned boolean array. |
java.lang.CharSequence |
getSrcText()
|
int |
getStyle()
Rendering style |
java.lang.String |
getValue(java.lang.String key)
Return the 1st value with the key. |
int |
getVisibleWhere()
e.g. |
java.lang.Object |
getWeakRef()
|
long |
getWhenCreated()
|
int |
getWhereFeatureLoadedFrom()
|
boolean |
isAmino()
|
boolean |
isEnabled()
|
static void |
loadResidueAnnotation(Protein p,
java.io.File file)
|
static java.lang.String |
mapKey(java.lang.String k)
|
int |
modificationCount()
|
void |
readFeatureAnnotations()
|
void |
removeEntry(ResidueAnnotation.Entry e)
|
java.lang.Object |
run(java.lang.String id,
java.lang.Object arg)
|
static java.io.File |
save(Protein p,
java.io.File dir)
|
void |
setColor(java.awt.Color c)
sets the color |
void |
setEnabled(boolean b)
|
void |
setEnabled(boolean b,
java.lang.String key)
|
void |
setFeatureName(java.lang.String name,
int featureSrc)
|
void |
setProtein(Protein p)
|
void |
setRendererText(java.lang.String s)
|
void |
setSelectedAminoacids(boolean[] bb,
int offset)
The method body may be kept empty. |
void |
setSelectedAminoacids(java.lang.String selection)
e.g. |
void |
setSelectedNucleotides(java.lang.String selection)
|
void |
setSrcText(java.lang.CharSequence t)
|
void |
setStyle(int i)
Rendering style |
void |
setValue(java.lang.String key,
java.lang.CharSequence textValue)
Adds a new key-value-pair |
void |
setVisibleWhere(int where)
|
boolean |
verifyDropRows(boolean drop,
java.lang.String data,
int row,
java.awt.Point screen)
|
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final java.lang.String NAME
public static final java.lang.String POS
public static final java.lang.String GROUP
public static final java.lang.String ATOMS
public static final java.lang.String STYLE
public static final java.lang.String TEXSHADE
public static final java.lang.String HYPERREFS
public static final java.lang.String COLOR
public static final java.lang.String BG_IMAGE
public static final java.lang.String VIEW3D
public static final java.lang.String SPECIFIC_VIEW3D
public static final java.lang.String DISABLED
public static final java.lang.String BALLOON
public static final java.lang.String[] MAIN_KEYS
public static final java.lang.String[] OTHER_KEYS
public static final ResidueAnnotation[] NONE
public static final long ENTRY_NOT_SAVED
Constructor Detail |
---|
public ResidueAnnotation(Protein p)
Method Detail |
---|
public java.lang.Object getWeakRef()
getWeakRef
in interface HasWeakRef
public int modificationCount()
modificationCount
in interface HasModiCount
public long getWhenCreated()
public void dispose()
dispose
in interface Disposable
public Protein getProtein()
getProtein
in interface HasProtein
getProtein
in interface ResidueSelection
getProtein
in interface SelectorOfNucleotides
public void setProtein(Protein p)
setProtein
in interface ResidueSelection
setProtein
in interface SelectorOfNucleotides
public java.lang.String getName()
getName
in interface HasName
public java.lang.String getID()
public void setSelectedAminoacids(boolean[] bb, int offset)
ResidueSelection
setSelectedAminoacids
in interface ResidueSelection
public void setSelectedAminoacids(java.lang.String selection)
public void setSelectedNucleotides(java.lang.String selection)
public int getSelectedAminoacidsOffset()
getSelectedAminoacidsOffset
in interface ResidueSelection
public boolean[] getSelectedAminoacids()
getSelectedAminoacids
in interface ResidueSelection
public int getSelectedNucleotidesOffset()
SelectorOfNucleotides
getSelectedNucleotidesOffset
in interface SelectorOfNucleotides
public boolean[] getSelectedNucleotides()
getSelectedNucleotides
in interface SelectorOfNucleotides
public int getStyle()
getStyle
in interface VisibleIn123
public void setStyle(int i)
setStyle
in interface VisibleIn123
public void setColor(java.awt.Color c)
setColor
in interface Colored
public java.awt.Color getColor()
getColor
in interface Colored
getColor
in interface VisibleIn123
public int getVisibleWhere()
VisibleIn123
getVisibleWhere
in interface VisibleIn123
public void setVisibleWhere(int where)
setVisibleWhere
in interface VisibleIn123
public java.awt.Image getImage(java.awt.Component observer)
getImage
in interface HasImage
public java.lang.Object run(java.lang.String id, java.lang.Object arg)
run
in interface ChRunnable
public javax.swing.ImageIcon getIcon()
public void setRendererText(java.lang.String s)
public java.lang.Object getRenderer(long options, long[] rendOptions)
getRenderer
in interface HasRenderer
public long getRendererModiCount()
getRendererModiCount
in interface HasRendererModiCount
public java.lang.String getValue(java.lang.String key)
public boolean isAmino()
public void setValue(java.lang.String key, java.lang.CharSequence textValue)
public void setEnabled(boolean b)
public void setEnabled(boolean b, java.lang.String key)
public ResidueAnnotation.Entry[] getEntries()
public void removeEntry(ResidueAnnotation.Entry e)
public void addE(java.lang.String key0, java.lang.String value)
public void addEnS(java.lang.String key0, java.lang.String value)
public void addE(long options, java.lang.String key, java.lang.String value, boolean isEnabled, int row)
public boolean isEnabled()
public static void loadResidueAnnotation(Protein p, java.io.File file)
public static java.io.File save(Protein p, java.io.File dir)
public java.util.Map getPropertyMap(boolean create)
getPropertyMap
in interface HasPropertyMap
public void readFeatureAnnotations()
public void setFeatureName(java.lang.String name, int featureSrc)
public java.lang.String getFeatureName()
public int getWhereFeatureLoadedFrom()
public java.lang.String getCssClass()
public java.lang.CharSequence getSrcText()
public void setSrcText(java.lang.CharSequence t)
public boolean featureEndsWithAminoName()
public boolean verifyDropRows(boolean drop, java.lang.String data, int row, java.awt.Point screen)
public static java.lang.String mapKey(java.lang.String k)
|
'STRAP:multiple sequence alignments ' | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |