X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;fp=src%2Fjalview%2Fanalysis%2FAlignmentUtils.java;h=f470dc6b366937fe36dc64cae13faa74ef90e9e1;hb=b122ba188c2ffcbb302809bafc02058e355643ee;hp=6ab49b27575086a59ec507741236224830cdadcc;hpb=e91b3bef83f320e13c59ad5d21d69f0abf3d7507;p=jalview.git diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 6ab49b2..f470dc6 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -547,7 +547,7 @@ public class AlignmentUtils if (translated == null || !(aaRes == translated.charAt(0))) { // debug - // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": " + // jalview.bin.Console.outPrintln(("Mismatch at " + i + "/" + aaResidue + ": " // + codon + "(" + translated + ") != " + aaRes)); return false; } @@ -698,7 +698,7 @@ public class AlignmentUtils * unmapped position; treat like a gap */ sourceGapMappedLength += ratio; - // System.err.println("Can't align: no codon mapping to residue " + // jalview.bin.Console.errPrintln("Can't align: no codon mapping to residue " // + sourceDsPos + "(" + sourceChar + ")"); // return; continue; @@ -883,7 +883,7 @@ public class AlignmentUtils { if (protein.isNucleotide() || !dna.isNucleotide()) { - System.err.println("Wrong alignment type in alignProteinAsDna"); + jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna"); return 0; } List unmappedProtein = new ArrayList<>(); @@ -908,7 +908,7 @@ public class AlignmentUtils { if (protein.isNucleotide() || !dna.isNucleotide()) { - System.err.println("Wrong alignment type in alignProteinAsDna"); + jalview.bin.Console.errPrintln("Wrong alignment type in alignProteinAsDna"); return 0; } // todo: implement this @@ -988,7 +988,7 @@ public class AlignmentUtils .getLength() == mappedFromLength - 1); if (cdsLength != mappedToLength && !addStopCodon) { - System.err.println(String.format( + jalview.bin.Console.errPrintln(String.format( "Can't align cds as protein (length mismatch %d/%d): %s", cdsLength, mappedToLength, cdsSeq.getName())); } @@ -1162,7 +1162,7 @@ public class AlignmentUtils AlignedCodon codon = sequenceCodon.getValue(); if (codon.peptideCol > 1) { - System.err.println( + jalview.bin.Console.errPrintln( "Problem mapping protein with >1 unmapped start positions: " + seq.getName()); } @@ -2770,7 +2770,7 @@ public class AlignmentUtils fromRange[i + 1]); if (range == null) { - System.err.println("Error in mapping " + seqMap + " from " + jalview.bin.Console.errPrintln("Error in mapping " + seqMap + " from " + fromSeq.getName()); return false; }