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josemduartejosemduarte
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Javadoc fix: errors in aaprops and survival and modules
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Lines changed: 7 additions & 7 deletions

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‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java‎

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@@ -258,7 +258,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
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* Returns the net charge of sequence at pH 7. The sequence argument must be
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* a protein sequence consisting of only non-ambiguous characters.
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* The net charge will be computed using the approach stated in
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* <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge>here</a>
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* <a href="http://www.innovagen.se/custom-peptide-synthesis/peptide-property-calculator/peptide-property-calculator-notes.asp#NetCharge">here</a>
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*
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* pKa values used will be either
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* those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java‎

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@@ -103,8 +103,8 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
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* Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
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* Example: "1111122222"<br/>
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* For the above example,<br/>
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* position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
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* position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
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* position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
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* position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
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*
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* @param sequence
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* a protein sequence consisting of non-ambiguous characters only

‎biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java‎

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@@ -119,8 +119,8 @@ public static Map<ATTRIBUTE, Map<TRANSITION, Double>> getTransition(String seque
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* An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.<br/>
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* Example: "1111122222"<br/>
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* For the above example,<br/>
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* position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
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* position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
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* position of the GROUPING.GROUP1 &amp; DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)<br/>
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* position of the GROUPING.GROUP1 &amp; DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)<br/>
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*
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* @param sequence
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* a protein sequence consisting of non-ambiguous characters only

‎biojava-survival/src/main/java/org/biojava/nbio/survival/cox/CoxR.java‎

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@@ -75,7 +75,7 @@
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* weights(n) :case weights
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* init :initial estimate for the coefficients
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* eps :tolerance for convergence. Iteration continues until
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* the percent change in loglikelihood is <= eps.
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* the percent change in loglikelihood is &lt;= eps.
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* chol_tol : tolerance for the Cholesky decompostion
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* method : 0=Breslow, 1=Efron
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* doscale : 0=don't scale the X matrix, 1=scale the X matrix

‎biojava-survival/src/main/java/org/biojava/nbio/survival/data/WorkSheet.java‎

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@@ -1464,7 +1464,7 @@ static public WorkSheet readCSV(File f, char delimiter) throws Exception {
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/**
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* Read a CSV/Tab delimited file where you pass in the delimiter
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*
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* @param f
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* @param is
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* @param delimiter
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* @return
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* @throws Exception

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