X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fmetadata%2FLimit.html;h=a61f93735a4a6adbec16d5ec237bcfea2eff75d4;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=f2f409591e84d03f6eae781b0113e15c87b2ce40;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git diff --git a/website/full_javadoc/compbio/metadata/Limit.html b/website/full_javadoc/compbio/metadata/Limit.html index f2f4095..a61f937 100644 --- a/website/full_javadoc/compbio/metadata/Limit.html +++ b/website/full_javadoc/compbio/metadata/Limit.html @@ -2,12 +2,12 @@ - + Limit - + @@ -92,27 +92,28 @@ compbio.metadata
Class Limit<T> 
-java.lang.Object
+java.lang.Object
   extended by compbio.metadata.Limit<T>
Type Parameters:
T - the type of an executable for which this limit is defined.
-
public class Limit<T>
extends java.lang.Object
+
public class Limit<T>
extends Object

A value object containing a maximum number of sequences and a maximum average - sequence length for a preset. + sequence length for a preset. Also contains static method for determining the + number of sequence and their average length in the List

+
Version:
+
1.0 January 2010
Author:
-
pvtroshin - - Date January 2010
+
pvtroshin
See Also:
LimitsManager
@@ -129,15 +130,15 @@ A value object containing a maximum number of sequences and a maximum average Limit(int seqNumber, int seqLength, - java.lang.String preset) + String preset)
-            +          Instantiate the limit Limit(int seqNumber, int seqLength, - java.lang.String preset, + String preset, boolean isDefault)
@@ -156,7 +157,7 @@ A value object containing a maximum number of sequences and a maximum average  boolean -equals(java.lang.Object obj) +equals(Object obj)
            @@ -172,14 +173,14 @@ A value object containing a maximum number of sequences and a maximum average static int -getAvgSequenceLength(java.util.List<FastaSequence> data) +getAvgSequenceLength(List<FastaSequence> data)
          Calculates an average sequence length of the dataset - java.lang.String + String getPreset()
@@ -212,15 +213,15 @@ A value object containing a maximum number of sequences and a maximum average  boolean -isExceeded(java.util.List<FastaSequence> data) +isExceeded(List<FastaSequence> data)
          Checks if the number of sequences or their average length in the dataset - exceeds limits the values defined by this Limit + exceeds this limit. - java.lang.String + String toString()
@@ -230,10 +231,10 @@ A value object containing a maximum number of sequences and a maximum average   - + - +
Methods inherited from class java.lang.ObjectMethods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, waitgetClass, notify, notifyAll, wait, wait, wait
  @@ -254,8 +255,15 @@ Limit 
 public Limit(int seqNumber,
              int seqLength,
-             java.lang.String preset)
+ String preset) +
+
Instantiate the limit +

+
Parameters:
seqNumber - the maximum number of sequences allowed for calculation. + Required
seqLength - the average length of the sequence, optional
preset - the name of preset if any, optional +
Throws: +
IllegalArgumentException - if the seqNumber is not supplied or the seqLength is negative
@@ -264,7 +272,7 @@ Limit 
 public Limit(int seqNumber,
              int seqLength,
-             java.lang.String preset,
+             String preset,
              boolean isDefault)
@@ -282,7 +290,7 @@ public Limit(int seqNumber,

getPreset

-public java.lang.String getPreset()
+public String getPreset()
@@ -296,7 +304,8 @@ getAvgSeqLength public int getAvgSeqLength()
-
+ +
Returns:
the allowed average sequence length
@@ -307,7 +316,8 @@ getSeqNumber public int getSeqNumber()
-
+ +
Returns:
the maximum number of sequences allowed
@@ -318,7 +328,8 @@ isDefault public boolean isDefault()
-
+ +
Returns:
true is this is a default limit to be used, false otherwise
@@ -329,7 +340,7 @@ hashCode public int hashCode()
-
Overrides:
hashCode in class java.lang.Object
+
Overrides:
hashCode in class Object
@@ -340,10 +351,10 @@ public int hashCode()

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
@@ -354,10 +365,10 @@ public boolean equals(java.lang.Object obj)

toString

-public java.lang.String toString()
+public String toString()
-
Overrides:
toString in class java.lang.Object
+
Overrides:
toString in class Object
@@ -368,15 +379,23 @@ public java.lang.String toString()

isExceeded

-public boolean isExceeded(java.util.List<FastaSequence> data)
+public boolean isExceeded(List<FastaSequence> data)
Checks if the number of sequences or their average length in the dataset - exceeds limits the values defined by this Limit + exceeds this limit.

-
Parameters:
data - +
Parameters:
data - the dataset to measure
Returns:
true if a limit is exceeded (what is the dataset is larger then - the limit), false otherwise.
+ the limit), false otherwise. First check the number of sequences + in the dataset and if it exceeds the limit return true + irrespective of the average length. If the number of sequences in + the dataset is less than the limit and average length is defined, + then check whether the total number of letters (number of + sequence multiplied by the average sequence length) is greater + then the total number of letters in the dataset. Returns true if + the total number of letters in the dataset is greater than the + limit, false otherwise.
@@ -384,7 +403,7 @@ public boolean isExceeded(java.util.List<

getAvgSequenceLength

-public static int getAvgSequenceLength(java.util.List<FastaSequence> data)
+public static int getAvgSequenceLength(List<FastaSequence> data)
Calculates an average sequence length of the dataset