X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FSMERFSConstraints.html;fp=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2FSMERFSConstraints.html;h=4cdc043248df1f95d43a7195d6e173ca64e95b04;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html b/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html new file mode 100644 index 0000000..4cdc043 --- /dev/null +++ b/website/full_javadoc/compbio/data/sequence/SMERFSConstraints.html @@ -0,0 +1,429 @@ + + + + + + +SMERFSConstraints + + + + + + + + + + + + +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ +

+ +compbio.data.sequence +
+Enum SMERFSConstraints

+
+java.lang.Object
+  extended by java.lang.Enum<SMERFSConstraints>
+      extended by compbio.data.sequence.SMERFSConstraints
+
+
+
All Implemented Interfaces:
Serializable, Comparable<SMERFSConstraints>
+
+
+
+
public enum SMERFSConstraints
extends Enum<SMERFSConstraints>
+ + +

+Enumeration defining two constraints for SMERFS columns score calculation. + MAX_SCORE gives the highest core of all the windows the column belongs to. + MID_SCORE gives the window score to the column in the middle. +

+ +

+

+
Author:
+
Agnieszka Golicz & Peter Troshin
+
+
+ +

+ + + + + + + + + + + + + +
+Enum Constant Summary
MAX_SCORE + +
+           
MID_SCORE + +
+           
+  + + + + + + + + + + + + + + + + + + +
+Field Summary
+static SMERFSConstraintsDEFAULT_COLUMN_SCORE + +
+          Default column scoring schema
+static doubleDEFAULT_GAP_THRESHOLD + +
+          Default gap threshold value for SMERFS algorithm
+static intDEFAULT_WINDOW_SIZE + +
+          Default window size value for SMERFS algorithm
+  + + + + + + + + + + + + + + + + + + + +
+Method Summary
+static SMERFSConstraintsgetSMERFSColumnScore(String score) + +
+           
+static SMERFSConstraintsvalueOf(String name) + +
+          Returns the enum constant of this type with the specified name.
+static SMERFSConstraints[]values() + +
+          Returns an array containing the constants of this enum type, in +the order they are declared.
+  + + + + + + + +
Methods inherited from class java.lang.Enum
compareTo, equals, getDeclaringClass, hashCode, name, ordinal, toString, valueOf
+  + + + + + + + +
Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait
+  +

+ + + + + + + + +
+Enum Constant Detail
+ +

+MAX_SCORE

+
+public static final SMERFSConstraints MAX_SCORE
+
+
+
+
+
+ +

+MID_SCORE

+
+public static final SMERFSConstraints MID_SCORE
+
+
+
+
+ + + + + + + + +
+Field Detail
+ +

+DEFAULT_COLUMN_SCORE

+
+public static final SMERFSConstraints DEFAULT_COLUMN_SCORE
+
+
Default column scoring schema +

+

+
+
+
+ +

+DEFAULT_WINDOW_SIZE

+
+public static final int DEFAULT_WINDOW_SIZE
+
+
Default window size value for SMERFS algorithm +

+

+
See Also:
Constant Field Values
+
+
+ +

+DEFAULT_GAP_THRESHOLD

+
+public static final double DEFAULT_GAP_THRESHOLD
+
+
Default gap threshold value for SMERFS algorithm +

+

+
See Also:
Constant Field Values
+
+ + + + + + + + +
+Method Detail
+ +

+values

+
+public static SMERFSConstraints[] values()
+
+
Returns an array containing the constants of this enum type, in +the order they are declared. This method may be used to iterate +over the constants as follows: +
+for (SMERFSConstraints c : SMERFSConstraints.values())
+    System.out.println(c);
+
+

+

+ +
Returns:
an array containing the constants of this enum type, in +the order they are declared
+
+
+
+ +

+valueOf

+
+public static SMERFSConstraints valueOf(String name)
+
+
Returns the enum constant of this type with the specified name. +The string must match exactly an identifier used to declare an +enum constant in this type. (Extraneous whitespace characters are +not permitted.) +

+

+
Parameters:
name - the name of the enum constant to be returned. +
Returns:
the enum constant with the specified name +
Throws: +
IllegalArgumentException - if this enum type has no constant +with the specified name +
NullPointerException - if the argument is null
+
+
+
+ +

+getSMERFSColumnScore

+
+public static SMERFSConstraints getSMERFSColumnScore(String score)
+
+
+
+
+
+ +
+ + + + + + + + + + + + + + + + + + + +
+ + + + + + + + + + + + +
Overview  Package   Class  Use  Tree  Deprecated  Index  Help 
+		 + +
+ PREV CLASS  + NEXT CLASS + FRAMES   + NO FRAMES   +  + + + +
+ SUMMARY: NESTED | ENUM CONSTANTS | FIELD | METHOD +DETAIL: ENUM CONSTANTS | FIELD | METHOD
+ + + +
+ + +