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///////////////////////////////////////////////////////////////// |
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// |
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// Copyright (C) 2005 Affymetrix, Inc. |
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// |
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// This library is free software; you can redistribute it and/or modify |
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// it under the terms of the GNU Lesser General Public License as published |
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// by the Free Software Foundation; either version 2.1 of the License, |
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// or (at your option) any later version. |
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// |
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// This library is distributed in the hope that it will be useful, but |
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// WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY |
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// or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License |
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// for more details. |
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// |
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// You should have received a copy of the GNU Lesser General Public License |
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// along with this library; if not, write to the Free Software Foundation, Inc., |
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// 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
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// |
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///////////////////////////////////////////////////////////////// |
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package affymetrix.gcos.chp; |
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|
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/** A type to hold the force call, the call that the algorithm would have made |
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* if the thresholds were relaxed. |
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*/ |
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public class ForceCallType { |
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|
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|
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/** The force call was made due to no signal threshold. */ |
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public static final byte NO_SIGNAL_THR_FORCE_CALL = 'N'; |
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|
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/** The force call was made due to weak signal threshold. */ |
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public static final byte WEAK_SIGNAL_THR_FORCE_CALL = 'W'; |
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|
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/** The force call was made due to saturation level. */ |
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public static final byte SATURATION_LEVEL_FORCE_CALL = 'S'; |
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|
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/** The force call was made due to quality score threshold. */ |
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public static final byte QUALITY_SCORE_THR_FORCE_CALL = 'Q'; |
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|
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/** The force call was made due to failed both trace and sequence profiles. */ |
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public static final byte TRACE_AND_SEQUENCE_PROFILES_FORCE_CALL = 'F'; |
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|
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/** The force call was made due to base reliability threshold. */ |
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public static final byte RELIABILITY_THR_FORCE_CALL = 'B'; |
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|
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/** The position (index) of the call. */ |
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private int position; |
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|
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/** Gets the position of the call. |
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* @return The position. |
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*/ |
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public int getPosition() { return position; } |
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|
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/** Sets the position of the call. |
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* @param p The position. |
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*/ |
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public void setPosition(int p) { position = p; } |
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|
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/** The force call. */ |
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private char call; |
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|
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/** Gets the call. |
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* @return The call. |
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*/ |
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public char getCall() { return call; } |
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|
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/** Sets the call. |
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* @param c The call. |
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*/ |
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public void setCall(char c) { call = c; } |
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|
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/** The reason for the call. */ |
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private byte reason; |
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|
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/** Gets the reason of the call. |
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* @return The reason. |
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*/ |
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public byte getReason() { return reason; } |
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|
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/** Sets the reason of the call. |
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* @param r The reason. |
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*/ |
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public void setReason(byte r) { reason = r; } |
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|
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/** Creates a new instance of ForceCallType */ |
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public ForceCallType() { |
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position = 0; |
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call = ' '; |
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reason = ' '; |
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} |
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|
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/** Creates a new instance of ForceCallType */ |
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public ForceCallType(ForceCallType f) { |
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position = f.getPosition(); |
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call = f.getCall(); |
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reason = f.getReason(); |
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} |
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} |