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//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage is free software: you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation, either version 3 of the License, or
//(at your option) any later version.
//Bandage is distributed in the hope that it will be useful,
//but WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//GNU General Public License for more details.
//You should have received a copy of the GNU General Public License
//along with Bandage. If not, see <http://www.gnu.org/licenses/>.
#include "blasthit.h"
#include "../graph/debruijnnode.h"
#include "blastquery.h"
#include "../program/settings.h"
#include "../program/globals.h"
#include <math.h>
BlastHit::BlastHit(BlastQuery * query, DeBruijnNode * node,
double percentIdentity, int alignmentLength,
int numberMismatches, int numberGapOpens,
int queryStart, int queryEnd,
int nodeStart, int nodeEnd,
SciNot eValue, double bitScore) :
m_query(query), m_node(node),
m_percentIdentity(percentIdentity), m_alignmentLength(alignmentLength),
m_numberMismatches(numberMismatches), m_numberGapOpens(numberGapOpens),
m_queryStart(queryStart), m_queryEnd(queryEnd),
m_nodeStart(nodeStart), m_nodeEnd(nodeEnd),
m_eValue(eValue), m_bitScore(bitScore)
{
int nodeLength = m_node->getLength();
int queryLength = m_query->getLength();
m_nodeStartFraction = double(nodeStart - 1) / nodeLength;
m_nodeEndFraction = double(nodeEnd) / nodeLength;
m_queryStartFraction = double(queryStart - 1) / queryLength;
m_queryEndFraction = double(queryEnd) / queryLength;
}
std::vector<BlastHitPart> BlastHit::getBlastHitParts(bool reverse, double scaledNodeLength)
{
std::vector<BlastHitPart> returnVector;
//If the colour scheme is Blast rainbow, then this function generates lots
//of BlastHitParts - each small and with a different colour of the rainbow.
if (g_settings->nodeColourScheme == BLAST_HITS_RAINBOW_COLOUR)
{
double scaledHitLength = (m_nodeEndFraction - m_nodeStartFraction) * scaledNodeLength;
int partCount = ceil(g_settings->blastRainbowPartsPerQuery * fabs(m_queryStartFraction - m_queryEndFraction));
//If there are way more parts than the scaled hit length, that means
//that a single part will be much less than a pixel in length. This
//isn't desirable, so reduce the partCount in these cases.
if (partCount > scaledHitLength * 2.0)
partCount = int(scaledHitLength * 2.0);
double nodeSpacing = (m_nodeEndFraction - m_nodeStartFraction) / partCount;
double querySpacing = (m_queryEndFraction - m_queryStartFraction) / partCount;
double nodeFraction = m_nodeStartFraction;
double queryFraction = m_queryStartFraction;
for (int i = 0; i < partCount; ++i)
{
QColor dotColour;
dotColour.setHsvF(queryFraction * 0.9, 1.0, 1.0); //times 0.9 to keep the colour from getting too close to red, as that could confuse the end with the start
double nextFraction = nodeFraction + nodeSpacing;
if (reverse)
returnVector.push_back(BlastHitPart(dotColour, 1.0 - nodeFraction, 1.0 - nextFraction));
else
returnVector.push_back(BlastHitPart(dotColour, nodeFraction, nextFraction));
nodeFraction = nextFraction;
queryFraction += querySpacing;
}
}
//If the colour scheme is Blast solid, then this function generates only one
//BlastHitPart with a colour dependent on the Blast query.
else
{
if (reverse)
returnVector.push_back(BlastHitPart(m_query->getColour(), 1.0 - m_nodeStartFraction, 1.0 - m_nodeEndFraction));
else
returnVector.push_back(BlastHitPart(m_query->getColour(), m_nodeStartFraction, m_nodeEndFraction));
}
return returnVector;
}
bool BlastHit::compareTwoBlastHitPointers(BlastHit * a, BlastHit * b)
{
return a->m_queryStart < b->m_queryStart;
}
double BlastHit::getQueryCoverageFraction()
{
int queryRegionSize = m_queryEnd - m_queryStart + 1;
int queryLength = m_query->getLength();
if (queryLength == 0)
return 0.0;
else
return double(queryRegionSize) / queryLength;
}
GraphLocation BlastHit::getHitStart() const
{
return GraphLocation(m_node, m_nodeStart);
}
GraphLocation BlastHit::getHitEnd() const
{
return GraphLocation(m_node, m_nodeEnd);
}
//This function returns the node sequence for this hit.
QByteArray BlastHit::getNodeSequence() const
{
int nodeSequenceLength = m_nodeEnd - m_nodeStart + 1;
return m_node->getSequence().mid(m_nodeStart-1, nodeSequenceLength);
}
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