X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FFastaSequence.html;h=1975623e0633c0788d4b58eda0083ccb457dcc00;hb=5f582fe1adafda5df440d1d1b3955b2bca7fbc88;hp=46890d982d2f549c66c0e6c5b692cb871dd9d5d6;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html index 46890d9..1975623 100644 --- a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html +++ b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html @@ -2,12 +2,12 @@ - + FastaSequence - + @@ -55,8 +55,8 @@ function windowTitle() - PREV CLASS  - NEXT CLASS + PREV CLASS  + NEXT CLASS FRAMES    NO FRAMES   @@ -92,28 +92,32 @@ compbio.data.sequence
Class FastaSequence 
-java.lang.Object
+java.lang.Object
   extended by compbio.data.sequence.FastaSequence
+
+
Direct Known Subclasses:
AnnotatedSequence
+
@Immutable
-public class FastaSequence
extends java.lang.Object
+public class FastaSequence
extends Object

A FASTA formatted sequence. Please note that this class does not make any - assumptions as to what sequence it store e.g. it could be nucleotide, protein - or even gapped alignment sequence! The only guarantee it makes is that the - sequence does not contain white space characters e.g. spaces, new lines etc + assumptions as to what sequence it stores e.g. it could be nucleotide, + protein or even gapped alignment sequence! The only guarantee it makes is + that the sequence does not contain white space characters e.g. spaces, new + lines etc

+
Version:
+
1.0 September 2009
Author:
-
pvtroshin - - Date September 2009
+
pvtroshin
@@ -128,8 +132,8 @@ A FASTA formatted sequence. Please note that this class does not make any Constructor Summary -FastaSequence(java.lang.String id, - java.lang.String sequence) +FastaSequence(String id, + String sequence)
          Upon construction the any whitespace characters are removed from the @@ -148,8 +152,8 @@ A FASTA formatted sequence. Please note that this class does not make any static int -countMatchesInSequence(java.lang.String theString, - java.lang.String theRegExp) +countMatchesInSequence(String theString, + String theRegExp)
            @@ -157,14 +161,14 @@ A FASTA formatted sequence. Please note that this class does not make any  boolean -equals(java.lang.Object obj) +equals(Object obj)
            - java.lang.String + String getFormatedSequence(int width)
@@ -172,7 +176,7 @@ A FASTA formatted sequence. Please note that this class does not make any - java.lang.String + String getFormattedFasta()
@@ -180,7 +184,7 @@ A FASTA formatted sequence. Please note that this class does not make any - java.lang.String + String getId()
@@ -196,7 +200,7 @@ A FASTA formatted sequence. Please note that this class does not make any - java.lang.String + String getOnelineFasta()
@@ -204,7 +208,7 @@ A FASTA formatted sequence. Please note that this class does not make any - java.lang.String + String getSequence()
@@ -212,7 +216,15 @@ A FASTA formatted sequence. Please note that this class does not make any - java.lang.String + int +hashCode() + +
+            + + + + String toString()
@@ -222,10 +234,10 @@ A FASTA formatted sequence. Please note that this class does not make any   - + - +
Methods inherited from class java.lang.ObjectMethods inherited from class java.lang.Object
getClass, hashCode, notify, notifyAll, wait, wait, waitgetClass, notify, notifyAll, wait, wait, wait
  @@ -244,8 +256,8 @@ A FASTA formatted sequence. Please note that this class does not make any

FastaSequence

-public FastaSequence(java.lang.String id,
-                     java.lang.String sequence)
+public FastaSequence(String id, + String sequence)
Upon construction the any whitespace characters are removed from the sequence @@ -267,7 +279,7 @@ public FastaSequence(java.lang.String id,

getId

-public java.lang.String getId()
+public String getId()
Gets the value of id

@@ -281,7 +293,7 @@ public java.lang.String getId()

getSequence

-public java.lang.String getSequence()
+public String getSequence()
Gets the value of sequence

@@ -295,8 +307,8 @@ public java.lang.String getSequence()

countMatchesInSequence

-public static int countMatchesInSequence(java.lang.String theString,
-                                         java.lang.String theRegExp)
+public static int countMatchesInSequence(String theString, + String theRegExp)
@@ -307,7 +319,7 @@ public static int countMatchesInSequence(java.lang.String theString,

getFormattedFasta

-public java.lang.String getFormattedFasta()
+public String getFormattedFasta()
@@ -318,7 +330,7 @@ public java.lang.String getFormattedFasta()

getOnelineFasta

-public java.lang.String getOnelineFasta()
+public String getOnelineFasta()
@@ -331,7 +343,7 @@ public java.lang.String getOnelineFasta()

getFormatedSequence

-public java.lang.String getFormatedSequence(int width)
+public String getFormatedSequence(int width)
Format sequence per width letter in one string. Without spaces.

@@ -357,12 +369,26 @@ public int getLength()

toString

-public java.lang.String toString()
+public String toString()
Same as oneLineFasta

-
Overrides:
toString in class java.lang.Object
+
Overrides:
toString in class Object
+
+
+
+
+
+
+ +

+hashCode

+
+public int hashCode()
+
+
+
Overrides:
hashCode in class Object
@@ -373,10 +399,10 @@ public java.lang.String toString()

equals

-public boolean equals(java.lang.Object obj)
+public boolean equals(Object obj)
-
Overrides:
equals in class java.lang.Object
+
Overrides:
equals in class Object
@@ -413,8 +439,8 @@ public boolean equals(java.lang.Object obj) - PREV CLASS  - NEXT CLASS + PREV CLASS  + NEXT CLASS FRAMES    NO FRAMES