'STRAP:multiple sequence alignments '

charite.christo
Class BA

java.lang.Object
  extended by charite.christo.BA
All Implemented Interfaces:
ChRunnable, HasModiCount, HasPropertyMap, java.lang.CharSequence, java.lang.Comparable

public final class BA
extends java.lang.Object
implements java.lang.CharSequence, java.lang.Comparable, ChRunnable, HasModiCount, HasPropertyMap


Field Summary
static int ERROR_PERMISSION_DENIED_BY_USER
           
static int OPTION_CACHE_TO_STRG
           
static int OPTION_IS_FILTERED
           
static long STRING_POOL
           
static long STRING_TRIM
           
 
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
BA(byte[] bb)
           
BA(byte[] bb, int from, int to)
           
BA(java.lang.CharSequence cs)
           
BA(int l)
           
 
Method Summary
 BA a(boolean b)
           
 BA a(boolean yesNo, java.lang.Object a)
           
 BA a(char ch)
           
 BA a(char ch, int times)
           
 BA a(double f)
           
 BA a(double number, int wInt, int wFrac)
           
 BA a(float f)
           
 BA a(long num)
           
 BA a(long num, int width)
           
 BA a(java.lang.Object s)
           
 BA a(java.lang.Object o, int from, int to)
           
 BA a1(java.lang.Object s)
           
 BA aBigFloat(double f, int precision)
           
 BA aFloat(double f, int precision)
           
 BA aHex(long rgb, int digits)
           
 BA aIfSze(int minSize, java.lang.Object a1, java.lang.Object a2)
           
 BA aln(char c)
           
 BA aln(java.lang.Object s)
           
 BA and(char c, java.lang.Object a)
           
 BA and(java.lang.Object a, char c)
           
 BA and(java.lang.Object a1, java.lang.Object a2)
           
 BA and(java.lang.Object a1, java.lang.Object a2, java.lang.Object a3)
           
 BA aQuoteIfNecessary(java.lang.Object o)
           
 BA aRplc(char c, char replacement, java.lang.Object o)
           
 BA aRplc(long options, java.lang.Object pattern, java.lang.Object replacement, java.lang.CharSequence txt)
           
 BA aRplc(java.lang.Object txt, java.lang.Object replacement, TextMatches matches)
           
 BA aSomeBytes(long n, int num)
           
 int begin()
          First text position +1
 BA boolToText(boolean[] bb, int offset, java.lang.String sep, java.lang.String intervall)
           
 BA boolToText(long bb, int offset, java.lang.String intervall)
           
 byte[] bytes()
          The byte array used internally to store the text;
 char charAt(int i)
           
 BA clr()
           
 int compareTo(java.lang.Object anotherString)
           
 int countAnsiEscapes()
           
 BA delBlanksL()
           
 BA delBlanksR()
           
 BA delSuffix(java.lang.String s)
           
 int end()
          Last text position +1
 BA enlargeCapacityBy(int reserve, int growPercent)
           
 byte[] ensureCapacity(int n)
           
 int[] eol()
          Line ends.
 boolean equals(java.lang.Object o)
           
static BA error(int type)
           
 BA filter(long option, int charClass, java.lang.Object o)
           
 BA filter(long option, int charClass, java.lang.Object text, int fromPosition, int toPosition)
           
 BA filter(long option, java.lang.Object o)
           
 BA format10(long num, int wInt)
           
 BA formatSize(java.io.File f)
           
 BA formatSize(int L)
           
 long[] getAnsiEscapes()
           
 int getOptions()
           
 java.util.Map getPropertyMap(boolean create)
           
 java.lang.Object getSendTo()
           
 java.lang.String getString(long options, int from, int to)
           
 ChTextView getTextView(boolean create)
           
 int hashCode()
           
 BA highlightButton()
           
 int idxToRow(int position)
           
 BA insert(int pos0, java.lang.Object strg)
           
 BA insertChars(int pos0, char ch, int times)
           
 BA insertI(int pos, int num)
           
 void insidePreTags()
           
static boolean isError(BA ba)
           
 BA join(java.lang.Object oo)
           
 BA join(java.lang.Object collectionOrArray, java.lang.String glue)
           
 BA join2(java.lang.String glueL, java.lang.Object collectionOrArray, java.lang.String glueR)
           
 BA joinBreakLines(java.lang.Object[] ss, java.lang.String glue, int foldInitWidth, int foldWidth, java.lang.String lineBreak)
           
 int length()
           
 int modificationCount()
           
 byte[] newBytes()
          returns the text between begin() and end()
 byte[] newBytes(int b, int e)
           
 java.lang.String newString(int from, int to)
           
 java.lang.String newStringToGt(int from)
           
 java.lang.String newStringTrim(int from, int to)
           
 boolean onlyWhiteSpace()
           
 BA or(java.lang.Object a1, java.lang.Object a2)
           
 BA or(java.lang.Object a1, java.lang.Object a2, java.lang.Object a3)
           
 BA removeLeadingSpace()
           
 BA replace(ChTextReplacement r)
           
 BA replace(long options, java.lang.Object pattern, java.lang.Object replacement)
           
 BA replace(long options, java.lang.Object pattern, java.lang.Object replacement, int from, int to)
           
 BA replaceChar(char c, char replacement)
           
 BA replaceChar(char c, char replacement, int from, int to)
           
 BA replaceRange(int from, int to0, java.lang.Object replacement)
           
 BA rmFirstLastChar(char cFirst, char cLast)
           
 java.lang.Object run(java.lang.String id, java.lang.Object arg)
           
 BA send()
           
 BA sendLater(int afterMS)
           
 BA set(byte[] bb, int b, int e)
           
 BA setBegin(int index)
           
 void setCharsAt(int b, int e, byte c)
           
 BA setEnd(int index)
           
 BA setFilterOptions(int o)
           
 BA setOptions(int o)
           
 BA setSendTo(java.lang.Object viewOrFile)
           
 void setTextSegment(javax.swing.text.Segment s)
           
 BA subSequence(int start, int end)
           
 byte[] subSequenceAsBytes(int start, int end)
           
 java.lang.Thread thread_send()
           
 java.lang.String toString()
           
 BA trimSize()
           
 void write(java.io.OutputStream os)
           
 
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
 

Field Detail

OPTION_IS_FILTERED

public static final int OPTION_IS_FILTERED
See Also:
Constant Field Values

OPTION_CACHE_TO_STRG

public static final int OPTION_CACHE_TO_STRG
See Also:
Constant Field Values

STRING_POOL

public static final long STRING_POOL
See Also:
Constant Field Values

STRING_TRIM

public static final long STRING_TRIM
See Also:
Constant Field Values

ERROR_PERMISSION_DENIED_BY_USER

public static final int ERROR_PERMISSION_DENIED_BY_USER
See Also:
Constant Field Values
Constructor Detail

BA

public BA(byte[] bb)

BA

public BA(byte[] bb,
          int from,
          int to)

BA

public BA(int l)

BA

public BA(java.lang.CharSequence cs)
Method Detail

setOptions

public BA setOptions(int o)

setFilterOptions

public BA setFilterOptions(int o)

setBegin

public BA setBegin(int index)

clr

public BA clr()

setEnd

public BA setEnd(int index)

set

public BA set(byte[] bb,
              int b,
              int e)

setCharsAt

public void setCharsAt(int b,
                       int e,
                       byte c)

getOptions

public int getOptions()

begin

public int begin()
First text position +1


end

public int end()
Last text position +1


bytes

public byte[] bytes()
The byte array used internally to store the text;


eol

public int[] eol()
Line ends. Indices of the '\n'. If trailing '\n' is missing inlcude also text-length+1 .


countAnsiEscapes

public int countAnsiEscapes()

getAnsiEscapes

public long[] getAnsiEscapes()

insidePreTags

public void insidePreTags()

delBlanksL

public BA delBlanksL()

delBlanksR

public BA delBlanksR()

trimSize

public BA trimSize()

newBytes

public byte[] newBytes()
returns the text between begin() and end()


newBytes

public byte[] newBytes(int b,
                       int e)

newString

public java.lang.String newString(int from,
                                  int to)

newStringTrim

public java.lang.String newStringTrim(int from,
                                      int to)

newStringToGt

public java.lang.String newStringToGt(int from)

getString

public java.lang.String getString(long options,
                                  int from,
                                  int to)

idxToRow

public int idxToRow(int position)

modificationCount

public int modificationCount()
Specified by:
modificationCount in interface HasModiCount

setTextSegment

public void setTextSegment(javax.swing.text.Segment s)

onlyWhiteSpace

public boolean onlyWhiteSpace()

enlargeCapacityBy

public BA enlargeCapacityBy(int reserve,
                            int growPercent)

a

public BA a(long num)

a

public BA a(char ch)

insertChars

public BA insertChars(int pos0,
                      char ch,
                      int times)

a

public BA a(char ch,
            int times)

aSomeBytes

public BA aSomeBytes(long n,
                     int num)

a

public BA a(double f)

a

public BA a(float f)

aFloat

public BA aFloat(double f,
                 int precision)

aBigFloat

public BA aBigFloat(double f,
                    int precision)

join

public BA join(java.lang.Object oo)

join

public BA join(java.lang.Object collectionOrArray,
               java.lang.String glue)

join2

public BA join2(java.lang.String glueL,
                java.lang.Object collectionOrArray,
                java.lang.String glueR)

joinBreakLines

public BA joinBreakLines(java.lang.Object[] ss,
                         java.lang.String glue,
                         int foldInitWidth,
                         int foldWidth,
                         java.lang.String lineBreak)

aln

public BA aln(java.lang.Object s)

aln

public BA aln(char c)

a

public BA a(java.lang.Object s)

a

public BA a(boolean b)

a

public BA a(java.lang.Object o,
            int from,
            int to)

filter

public BA filter(long option,
                 java.lang.Object o)

filter

public BA filter(long option,
                 int charClass,
                 java.lang.Object o)

filter

public BA filter(long option,
                 int charClass,
                 java.lang.Object text,
                 int fromPosition,
                 int toPosition)

a

public BA a(boolean yesNo,
            java.lang.Object a)

and

public BA and(java.lang.Object a,
              char c)

and

public BA and(char c,
              java.lang.Object a)

and

public BA and(java.lang.Object a1,
              java.lang.Object a2)

and

public BA and(java.lang.Object a1,
              java.lang.Object a2,
              java.lang.Object a3)

aIfSze

public BA aIfSze(int minSize,
                 java.lang.Object a1,
                 java.lang.Object a2)

or

public BA or(java.lang.Object a1,
             java.lang.Object a2)

or

public BA or(java.lang.Object a1,
             java.lang.Object a2,
             java.lang.Object a3)

a1

public BA a1(java.lang.Object s)

format10

public BA format10(long num,
                   int wInt)

formatSize

public BA formatSize(java.io.File f)

formatSize

public BA formatSize(int L)

a

public BA a(long num,
            int width)

a

public BA a(double number,
            int wInt,
            int wFrac)

ensureCapacity

public byte[] ensureCapacity(int n)

aHex

public BA aHex(long rgb,
               int digits)

aQuoteIfNecessary

public BA aQuoteIfNecessary(java.lang.Object o)

replace

public BA replace(ChTextReplacement r)

aRplc

public BA aRplc(char c,
                char replacement,
                java.lang.Object o)

replaceChar

public BA replaceChar(char c,
                      char replacement)

replaceChar

public BA replaceChar(char c,
                      char replacement,
                      int from,
                      int to)

replace

public BA replace(long options,
                  java.lang.Object pattern,
                  java.lang.Object replacement)

replace

public BA replace(long options,
                  java.lang.Object pattern,
                  java.lang.Object replacement,
                  int from,
                  int to)

replaceRange

public BA replaceRange(int from,
                       int to0,
                       java.lang.Object replacement)

insert

public BA insert(int pos0,
                 java.lang.Object strg)

insertI

public BA insertI(int pos,
                  int num)

rmFirstLastChar

public BA rmFirstLastChar(char cFirst,
                          char cLast)

aRplc

public BA aRplc(java.lang.Object txt,
                java.lang.Object replacement,
                TextMatches matches)

aRplc

public BA aRplc(long options,
                java.lang.Object pattern,
                java.lang.Object replacement,
                java.lang.CharSequence txt)

delSuffix

public BA delSuffix(java.lang.String s)

write

public void write(java.io.OutputStream os)
           throws java.io.IOException
Throws:
java.io.IOException

toString

public java.lang.String toString()
Specified by:
toString in interface java.lang.CharSequence
Overrides:
toString in class java.lang.Object

charAt

public char charAt(int i)
Specified by:
charAt in interface java.lang.CharSequence

length

public int length()
Specified by:
length in interface java.lang.CharSequence

subSequence

public BA subSequence(int start,
                      int end)
Specified by:
subSequence in interface java.lang.CharSequence

subSequenceAsBytes

public byte[] subSequenceAsBytes(int start,
                                 int end)

equals

public boolean equals(java.lang.Object o)
Overrides:
equals in class java.lang.Object

compareTo

public int compareTo(java.lang.Object anotherString)
Specified by:
compareTo in interface java.lang.Comparable

hashCode

public int hashCode()
Overrides:
hashCode in class java.lang.Object

removeLeadingSpace

public BA removeLeadingSpace()

boolToText

public BA boolToText(boolean[] bb,
                     int offset,
                     java.lang.String sep,
                     java.lang.String intervall)

boolToText

public BA boolToText(long bb,
                     int offset,
                     java.lang.String intervall)

run

public java.lang.Object run(java.lang.String id,
                            java.lang.Object arg)
Specified by:
run in interface ChRunnable

error

public static BA error(int type)

isError

public static boolean isError(BA ba)

getPropertyMap

public java.util.Map getPropertyMap(boolean create)
Specified by:
getPropertyMap in interface HasPropertyMap

highlightButton

public BA highlightButton()

setSendTo

public BA setSendTo(java.lang.Object viewOrFile)

getSendTo

public java.lang.Object getSendTo()

send

public BA send()

thread_send

public java.lang.Thread thread_send()

sendLater

public BA sendLater(int afterMS)

getTextView

public ChTextView getTextView(boolean create)

'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, Protein and StrapEvent.'